guyteichman / rnalysis Goto Github PK

RNA sequencing analysis software

Home Page: https://guyteichman.github.io/RNAlysis

License: MIT License

Python 98.76% Makefile 0.10% Batchfile 0.03% R 1.10% Rebol 0.01%

rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna

rnalysis's Introduction

What is RNAlysis?

RNAlysis is a Python-based software for analyzing RNA sequencing data. RNAlysis allows you to build customized analysis pipelines suiting your specific research questions, going all the way from exploratory data analysis and data visualization through clustering analysis and gene-set enrichment analysis.

What can I do with RNAlysis?

Filter your gene expression matrices, differential expression tables, fold change data, and tabular data in general.
Normalize your gene expression matrices
Visualise, explore and describe your sequencing data
Find global relationships between sample expression profiles with clustering analyses and dimensionality reduction
Create and share analysis pipelines
Perform enrichment analysis with pre-determined Gene Ontology terms/KEGG pathways, or with used-defined attributes
Perform enrichment analysis on a single ranked list of genes, instead of a test set and a background set

To get an overview of what RNAlysis can do, read the tutorial and the user guide.

RNAlysis supports gene expression matrices and differential expression tables in general, and integrates in particular with Python's HTSeq-count and R's DESeq2.

How do I install it?

You can either install RNAlysis as a stand-alone app, or via PyPI. To learn how to install RNAlysis, visit the Installation page.

How do I use it?

If you installed RNAlysis as a stand-alone app, simply open the app ("RNAlysis.exe" on Windows, "RNAlysis.dmg" on MacOS) and wait for it to load (it may take a minute or two, so be patient!).

If you installed RNAlysis from PyPi, you can launch RNAlysis by typing the following command:

rnalysis-gui

Or through a python console:

>>> from rnalysis import gui
>>> gui.run_gui()

In addition, you can write Python code that uses RNAlysis functions as described in the programmatic interface user guide.

Dependencies

All of RNAlysis's dependencies can be installed automatically via PyPI.

Credits

How do I cite RNAlysis?

If you use RNAlysis in your research, please cite:

Teichman, G., Cohen, D., Ganon, O., Dunsky, N., Shani, S., Gingold, H., and Rechavi, O. (2023).
RNAlysis: analyze your RNA sequencing data without writing a single line of code. BMC Biology, 21, 74.
https://doi.org/10.1186/s12915-023-01574-6

If you use the CutAdapt adapter trimming tool in your research, please cite:

Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads.
EMBnet.journal, 17(1), pp. 10-12.
https://doi.org/10.14806/ej.17.1.200

If you use the kallisto RNA sequencing quantification tool in your research, please cite:

Bray, N., Pimentel, H., Melsted, P. et al.
Near-optimal probabilistic RNA-seq quantification.
Nat Biotechnol 34, 525–527 (2016).
https://doi.org/10.1038/nbt.3519

If you use the bowtie2 aligner in your research, please cite:

Langmead, B., and Salzberg, S.L. (2012).
Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012 94 9, 357–359.
https://doi.org/10.1038/nmeth.1923

If you use the ShortStack aligner in your research, please cite:

Axtell, MJ. (2013).
ShortStack: Comprehensive annotation and quantification of small RNA genes. RNA 19:740-751.
https://doi.org/10.1261/rna.035279.112

If you use the DESeq2 differential expression tool in your research, please cite:

Love MI, Huber W, Anders S (2014).
“Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.”
Genome Biology, 15, 550.
https://doi.org/10.1186/s13059-014-0550-8

If you use the Limma-Voom differential expression pipeline in your research, please cite:

Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015).
limma powers differential expression analyses for RNA-sequencing and microarray studies.
Nucleic Acids Res. 43, e47–e47.
https://doi.org/10.1093/nar/gkv007

Law, C.W., Chen, Y., Shi, W., and Smyth, G.K. (2014).
Voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
Genome Biol. 15, 1–17.
https://doi.org/10.1186/gb-2014-15-2-r29

If you use the HDBSCAN clustering feature in your research, please cite:

 L. McInnes, J. Healy, S. Astels, hdbscan: Hierarchical density based clustering In:
Journal of Open Source Software, The Open Journal, volume 2, number 11. 2017
https://doi.org/10.1371/journal.pcbi.0030039

If you use the XL-mHG single-set enrichment test in your research, please cite:

Eden, E., Lipson, D., Yogev, S., and Yakhini, Z. (2007).
 Discovering Motifs in Ranked Lists of DNA Sequences. PLOS Comput. Biol. 3, e39.
https://doi.org/10.1371/journal.pcbi.0030039>doi.org/10.1371/journal.pcbi.0030039</a>

Wagner, F. (2017). The XL-mHG test for gene set enrichment. ArXiv.
https://doi.org/10.48550/arXiv.1507.07905

If you use the Ensembl database in your research, please cite:

Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov AG, Barnes I, et al.
Ensembl 2023. Nucleic Acids Res [Internet]. 2023 Jan 6;51(D1):D933–41.
doi.org/10.1093/nar/gkac958

If you use the PANTHER database in your research, please cite:

Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou L-P, Mi H.
PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci [Internet]. 2022 Jan 1;31(1):8–22.
doi.org/10.1002/pro.4218

If you use the OrthoInspector database in your research, please cite:

Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, et al.
OrthoInspector 3.0: open portal for comparative genomics. Nucleic Acids Res [Internet]. 2019 Jan 8;47(D1):D411–8.
doi.org/10.1093/nar/gky1068

If you use the PhylomeDB database in your research, please cite:

Fuentes D, Molina M, Chorostecki U, Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T.
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. Nucleic Acids Res [Internet]. 2022 Jan 7;50(D1):D1062–8.
doi.org/10.1093/nar/gkab966

If you use the UniProt gene ID mapping service in your research, please cite:

The UniProt Consortium.
UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res [Internet]. 2023 Jan 6;51(D1):D523–31.
doi.org/10.1093/nar/gkac1052

Development Lead

Guy Teichman: [email protected]

Contributors

Dror Cohen
Or Ganon
Netta Dunsky
Shachar Shani
Mintxoklet
Bipin Kumar
Matthias Wilm
sandyl27
clockgene
NeuroRookie

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

rnalysis's People

Contributors

Stargazers

Watchers

Forkers

depletionmode umutcanbozan hasihays genostack ihinne newgenia gonzo-likes lbgbox science64 miguel-montez kbipinkumar xingxingshen mynahub

rnalysis's Issues

Need assistance in running DESeq2

Describe the bug

Hello Guy,
I tried to run DESeq2 and I'm getting the following error
Traceback (most recent call last):

File "rnalysis\gui\gui.py", line 3697, in finish_generic_job

File "rnalysis\gui\gui_widgets.py", line 329, in run

File "rnalysis\filtering.py", line 2874, in differential_expression_deseq2

File "rnalysis\utils\differential_expression.py", line 130, in run_deseq2_analysis

File "rnalysis\utils\io.py", line 1397, in run_r_script

AssertionError: R script failed to execute (return code 1).

Steps To Reproduce

I need help to get over the error mentioned above.
Please do help me with this.

Expected behavior

No response

Screenshots

No response

How did you install RNAlysis?

Stand-alone app

RNAlysis version

3.7

Operating system

Windows

Additional context

No response

Bug Report: PCA analysis, ValueError: Data must not be constant

Describe the bug

Hey,

I tried to run a PCA plot but I get this error message:

Traceback (most recent call last):
File "rnalysis/gui/gui.py", line 1347, in apply_function
File "rnalysis/gui/gui.py", line 1970, in _apply_function_from_params
File "rnalysis/gui/gui.py", line 1356, in _apply_function_from_params
File "rnalysis/filtering.py", line 4401, in pca
File "rnalysis/utils/generic.py", line 71, in standard_box_cox
File "sklearn/utils/_set_output.py", line 142, in wrapped
File "sklearn/preprocessing/_data.py", line 3103, in fit_transform
File "sklearn/preprocessing/_data.py", line 3116, in _fit
File "sklearn/preprocessing/_data.py", line 3116, in
File "sklearn/preprocessing/_data.py", line 3274, in _box_cox_optimize
File "scipy/stats/_morestats.py", line 1099, in boxcox
ValueError: Data must not be constant.

Here is the header of my data file:
head.csv

I have seen that your Celegans file from the tutorial has no 0 but extremely small values. Is this the problem?

Steps To Reproduce

Loaded file
Visualize
Principal Component Analysis (PCA) plot
Apply

Expected behavior

No response

Screenshots

No response

How did you install RNAlysis?

Stand-alone app

RNAlysis version

3.6.0

Operating system

MacOS 12.7

Additional context

No response

RNAlysis.dmg not found

Hi, I just downloaded the file 'RNAlysis-3.5.2_macos.zip'. After unzipping I get a file named 'RNAlysis', but not the expected 'RNAlysis.dmg' file

Could you help me?

No such file or directory: latest_version.txt

When I run the gui, it turned out the error mentioned below:

from rnalysis import gui
gui.run_gui()
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\LY_N.conda\envs\rnaseq\lib\site-packages\rnalysis\gui_init_.py", line 8, in run_gui
main()
File "C:\Users\LY_N.conda\envs\rnaseq\lib\site-packages\rnalysis\gui\main.py", line 8, in main
asyncio.run(gui.run())
File "C:\Users\LY_N.conda\envs\rnaseq\lib\asyncio\runners.py", line 44, in run
return loop.run_until_complete(main)
File "C:\Users\LY_N.conda\envs\rnaseq\lib\asyncio\base_events.py", line 649, in run_until_complete
return future.result()
File "C:\Users\LY_N.conda\envs\rnaseq\lib\site-packages\rnalysis\gui\gui.py", line 4337, in run
if io.check_changed_version():
File "C:\Users\LY_N.conda\envs\rnaseq\lib\site-packages\rnalysis\utils\io.py", line 162, in check_changed_version
with open(filename, 'w') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\LY_N\AppData\Roaming\RNAlysis\RNAlysis\latest_version.txt'

To perform Quality control

Hello Guy,
I'm a beginner in bioinformatics.
Can you please tell me how can I run a FastQC or other similar tools to run a quality control
using RNAlysis?

(I use RNAlysis version 3.7.0 in Windows 11).

ValueError: No taxon ID could be matched to any of the given gene IDs

Describe the bug

Hello,

I used your pipeline and everythings works well but when i want to use Enrichment analysis i got my enrichment set and my background set i got this error: "ValueError: No taxon ID could be matched to any of the given gene IDs"

Is it because genes of my organism are not in database Gene Ontology ?

There is a way to execute Enrichment analysis if our genes are not referenced in the Gene ontology database ?

Steps To Reproduce

Enrichment Analysis

Expected behavior

No response

Screenshots

No response

How did you install RNAlysis?

Stand-alone app

RNAlysis version

3.9.2

Operating system

Linux

Additional context

No response

Issue with building RNAlysis under Archlinux

while trying to build RNAlysis from PyPI sources under archlinux i am encountering following error.

  $ python setup.py build

  File "/home/bipin/Share/test/rnalysis/src/RNAlysis-3.3.0/setup.py", line 38, in <module>
    with open('requirements.txt') as requirements_file:
FileNotFoundError: [Errno 2] No such file or directory: 'requirements.txt'

However, the issues don't seem to affect sources downloaded from GitHub. that said GitHub source download is huge (~700mb) compared to PyPi sources. any idea reason discrepancy?

also it would be great if PyPi sources could be fixed so that package can be built using the same

furthermore, there is also the issue of setup.py installing directory named tests into site-packages folder (i.e. /usr/lib/python3.10/site-packages/tests/) which is an undesirable behaviour per the wiki due to setuptools being misconfigured to include the directory containing its tests as a top level Python package.

this causes the resulting binary packages from being installed due file conflicts

$ sudo pacman -U rnalysis-3.3.0-1-any.pkg.tar.zst

error: failed to commit transaction (conflicting files)
rnalysis: /usr/lib/python3.10/site-packages/tests/__init__.py exists in filesystem (owned by python-pairwisedist)
rnalysis: /usr/lib/python3.10/site-packages/tests/__pycache__/__init__.cpython-310.opt-1.pyc exists in filesystem (owned by python-pairwisedist)
rnalysis: /usr/lib/python3.10/site-packages/tests/__pycache__/__init__.cpython-310.pyc exists in filesystem (owned by python-pairwisedist)

it would be great to have this behaviour fixed in setup.py itself.

Error during installation

Hello,

I am completely new to all things coding, so I am very excited to try RNAlysis. I believe that I have installed Python 3.8, pip, R 4.2.2, graphviz, and kallisto. The installation problem is probably on my end, but any advice would be appreciated.

% pip install RNAlysis[all]
zsh: no matches found: RNAlysis[all]

% pip install RNAlysis

Collecting RNAlysis
Using cached RNAlysis-3.3.0-py3-none-any.whl (19.9 MB)
Collecting numpy>=1.21.4
Using cached numpy-1.24.1-cp311-cp311-macosx_11_0_arm64.whl (13.8 MB)
Collecting pandas>=1.3.5
Using cached pandas-1.5.2-cp311-cp311-macosx_11_0_arm64.whl (10.7 MB)
Collecting matplotlib<3.6.0,>=3.4.2
Using cached matplotlib-3.5.3.tar.gz (35.2 MB)
Preparing metadata (setup.py) ... done
Collecting seaborn>=0.11.2
Using cached seaborn-0.12.2-py3-none-any.whl (293 kB)
Collecting statsmodels>=0.12.0
Using cached statsmodels-0.13.5-cp311-cp311-macosx_11_0_arm64.whl (9.2 MB)
Collecting scikit-learn>=1.0.0
Using cached scikit_learn-1.2.0-cp311-cp311-macosx_12_0_arm64.whl (8.3 MB)
Collecting grid-strategy>=0.0.1
Using cached grid_strategy-0.0.1-py3-none-any.whl (11 kB)
Collecting pyyaml>=6.0
Using cached PyYAML-6.0-cp311-cp311-macosx_11_0_arm64.whl (167 kB)
Collecting UpSetPlot>=0.6.1
Using cached UpSetPlot-0.8.0.tar.gz (22 kB)
Preparing metadata (setup.py) ... done
Collecting matplotlib-venn>=0.11.7
Using cached matplotlib-venn-0.11.7.tar.gz (29 kB)
Preparing metadata (setup.py) ... done
Collecting scipy>=1.7.2
Using cached scipy-1.10.0-cp311-cp311-macosx_12_0_arm64.whl (28.7 MB)
Collecting scikit-learn-extra>=0.2.0
Using cached scikit-learn-extra-0.2.0.tar.gz (813 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting pairwisedist>=1.2.0
Using cached pairwisedist-1.3.0-py2.py3-none-any.whl (14 kB)
Collecting requests>=2.24.0
Using cached requests-2.28.1-py3-none-any.whl (62 kB)
Collecting graphviz>=0.19.1
Using cached graphviz-0.20.1-py3-none-any.whl (47 kB)
Collecting joblib<1.2.0,>=1.1.0
Using cached joblib-1.1.1-py2.py3-none-any.whl (309 kB)
Collecting tqdm>=4.64
Using cached tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
Collecting appdirs>=1.4.0
Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting typing-extensions>=4.4
Using cached typing_extensions-4.4.0-py3-none-any.whl (26 kB)
Collecting PyQt5>=5.15.7
Using cached PyQt5-5.15.7.tar.gz (3.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [33 lines of output]
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 144, in prepare_metadata_for_build_wheel
hook = backend.prepare_metadata_for_build_wheel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'

  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
      main()
    File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 148, in prepare_metadata_for_build_wheel
      whl_basename = backend.build_wheel(metadata_directory, config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/folders/t9/j5z223l15tv0dy_n6nt9jmq40000gn/T/pip-build-env-wqvha_ul/overlay/lib/python3.11/site-packages/sipbuild/api.py", line 46, in build_wheel
      project = AbstractProject.bootstrap('wheel',
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/folders/t9/j5z223l15tv0dy_n6nt9jmq40000gn/T/pip-build-env-wqvha_ul/overlay/lib/python3.11/site-packages/sipbuild/abstract_project.py", line 87, in bootstrap
      project.setup(pyproject, tool, tool_description)
    File "/private/var/folders/t9/j5z223l15tv0dy_n6nt9jmq40000gn/T/pip-build-env-wqvha_ul/overlay/lib/python3.11/site-packages/sipbuild/project.py", line 585, in setup
      self.apply_user_defaults(tool)
    File "/private/var/folders/t9/j5z223l15tv0dy_n6nt9jmq40000gn/T/pip-install-qw5gcyn6/pyqt5_8f6e333c4e11463398cca7cd19fe7ac2/project.py", line 69, in apply_user_defaults
      super().apply_user_defaults(tool)
    File "/private/var/folders/t9/j5z223l15tv0dy_n6nt9jmq40000gn/T/pip-build-env-wqvha_ul/overlay/lib/python3.11/site-packages/pyqtbuild/project.py", line 70, in apply_user_defaults
      super().apply_user_defaults(tool)
    File "/private/var/folders/t9/j5z223l15tv0dy_n6nt9jmq40000gn/T/pip-build-env-wqvha_ul/overlay/lib/python3.11/site-packages/sipbuild/project.py", line 236, in apply_user_defaults
      self.builder.apply_user_defaults(tool)
    File "/private/var/folders/t9/j5z223l15tv0dy_n6nt9jmq40000gn/T/pip-build-env-wqvha_ul/overlay/lib/python3.11/site-packages/pyqtbuild/builder.py", line 69, in apply_user_defaults
      raise PyProjectOptionException('qmake',
  sipbuild.pyproject.PyProjectOptionException
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.

Thank you,
R

No module named 'cutadapt'

Describe the bug
when im trying to install fastq or GUI I get the error: No module named 'cutadapt'

Screenshots

Desktop (please complete the following information):
MacOs

Unable to run rnalysis-gui from a non root user in an HPC cluster.

Describe the bug

Hi,

I installed rnalysis using "pip install RNAlysis[all]" on a linux machine / on docker ubuntu container and
when trying to load rnalysis using rnalysis-gui /gui.run_gui() it hangs with no error.
It did work on some occasions on a docker container only when run from the root user which isn't
an option since we need to run the program as a regular user on the cluster .
any suggestions on how to debug this problem ?

Steps To Reproduce

singularity exec --writable /data/bin/singularity_images/python_RNAlysis1.sif /bin/bash
INFO: Converting SIF file to temporary sandbox...
WARNING: Skipping mount /etc/localtime [binds]: /etc/localtime doesn't exist in container
Singularity> python3
Python 3.10.12 (main, Jun 11 2023, 05:26:28) [GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

from rnalysis import gui
Warning: 'GraphViz' installation not found. If you want to generate Ontology and Pathway Graphs, Please install GraphViz and add it to PATH.
See https://graphviz.org/download/ for more information.
gui.run_gui()

Expected behavior

No response

Screenshots

How did you install RNAlysis?

installed via pip/Python

RNAlysis version

3.10

Operating system

Rocky linux \ docker container of ubuntu

Additional context

No response

Can´t get DEseq2 differential expression anallysis to work :(

Well I didnt really know where to post my issue since it is probably not a bug. With that being said, I was trying to perform differential expression from my count matrix generated with kallisto (and filtered). However an error pops up that says the following:
Traceback (most recent call last):
File "C:\Users\Jon\AppData\Local\Programs\Python\Python310\lib\site-packages\rnalysis\gui\gui.py", line 3425, in finish_generic_job
raise worker_output[0]
File "C:\Users\Jon\AppData\Local\Programs\Python\Python310\lib\site-packages\rnalysis\gui\gui_widgets.py", line 268, in run
result = self.partial()
File "C:\Users\Jon\AppData\Local\Programs\Python\Python310\lib\site-packages\rnalysis\filtering.py", line 2524, in differential_expression_deseq2
output_dir = differential_expression.run_deseq2_analysis(data_path, design_matrix, comparisons,
File "C:\Users\Jon\AppData\Local\Programs\Python\Python310\lib\site-packages\rnalysis\utils\differential_expression.py", line 55, in run_deseq2_analysis
io.run_r_script(script_path, r_installation_folder)
File "C:\Users\Jon\AppData\Local\Programs\Python\Python310\lib\site-packages\rnalysis\utils\io.py", line 1278, in run_r_script
assert not return_code, f"R script failed to execute (return code {return_code}). "
AssertionError: R script failed to execute (return code 1).

I hope maybe you can help me as I have absolutely no clue about how to solve it. Thank you very much and happy new year!

Needed guidance in installing bowtie2

Hii Guy,
I'm trying to install bowtie2 on my windows. I followed the bowtie2 manual to install it through MinGW. I installed make too. But now I'm stuck here since I don't know to compile bowtie2 tools using makefile. Can you please help me with this.
How can I get it installed to use along with RNAlysis?
And also can I use Rbowtie2 package in RNAlysis. Is that possible?
Looking forward to hearing from you as soon as possible.
Thank you.
Regards

Unable to run RNAlysis

Unable to run RNAlysis
I tried to run RNAlysis with the data given in the example part of user guide(analysis 1) as a sample run since I'm using this for first time. I was not able run it and getting the following errror which I attached as photo. Please do help me troubleshooting this.
Device version: Windows 10

DeSeq2 Error

Describe the bug

I'm attempting to run a DESeq2 differential expression analysis but am getting the following error:

R script failed to execute: 'Error in contrib.url(repos, "source") : trying to use CRAN without setting a mirror'. See full error report below.

Full error report:

RuntimeError: See R log below.
Installing package into 'C:/Users/hanna/AppData/Local/R/win-library/4.3'
(as 'lib' is unspecified)
Error in contrib.url(repos, "source") :
trying to use CRAN without setting a mirror
Calls: install.packages -> contrib.url
Execution halted

The above exception was the direct cause of the following exception:

Traceback (most recent call last):

File "rnalysis\gui\gui.py", line 4340, in finish_generic_job

File "rnalysis\gui\gui_widgets.py", line 382, in run

File "rnalysis\filtering.py", line 3204, in differential_expression_deseq2

File "rnalysis\utils\differential_expression.py", line 122, in run_deseq2_analysis

File "rnalysis\utils\installs.py", line 101, in install_deseq2

File "rnalysis\utils\io.py", line 2303, in run_r_script

ChildProcessError: R script failed to execute: 'Error in contrib.url(repos, "source") : trying to use CRAN without setting a mirror'. See full error report below.

Any assistance debugging this would be greatly appreciated, I'm not an R user so struggling to debug this issue.

Steps To Reproduce

Error appears when clicking 'Start DeSeq2' after inputting all information as described in the tutorial.

Expected behavior

No response

Screenshots

No response

How did you install RNAlysis?

Stand-alone app

RNAlysis version

3.11.0

Operating system

Windows 11

Additional context

No response

Unable to open csv through RNAlysis GUI

Describe the bug
Unable to open a csv through the RNAlysis GUI on Mac (Apple silicon)

To Reproduce
Steps to reproduce the behavior:

Made now conda environment with Python 3.9
Installed basic version of RNAlysis pip install RNAlysis
Open GUI with rnalysis-gui
Error: numba not installed; so pip install numba
Clicked on 'Load' in GUI and selected table
Following error comes on clicking on 'Start':
Traceback (most recent call last):
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/rnalysis/gui/gui.py", line 1893, in start
self.filter_obj = filter_obj_type(file_path, **kwargs)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/rnalysis/filtering.py", line 2137, in init
super().init(fname, drop_columns)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/rnalysis/filtering.py", line 97, in init
self.df = io.load_csv(fname, 0, squeeze=True, drop_columns=drop_columns)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/rnalysis/utils/io.py", line 228, in load_csv
df = pd.read_csv(filename, **kwargs)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/util/_decorators.py", line 211, in wrapper
return func(*args, **kwargs)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/util/_decorators.py", line 331, in wrapper
return func(*args, **kwargs)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
return _read(filepath_or_buffer, kwds)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 605, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1442, in init
self._engine = self._make_engine(f, self.engine)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1753, in _make_engine
return mapping[engine](f, **self.options)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 112, in init
self._make_reader(f)
File "/Users/vaibhavmahajan/opt/anaconda3/envs/RNAlysis/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 221, in _make_reader
self.buf.extend(list(line_rdr))
_csv.Error: line contains NUL
and the csv doesn't open.

Expected behavior
The csv opens through GUI

Note
I am a beginner and apologies if this was a simple issue and not meant to be raised here. But any solutions to this problem would be great. Thank you!

Bug Report: Failed to find R executable (MacOS stand-alone app)

Describe the bug

When I try to run the DESeq2 program, the module tries to detect the folder where the R executable is installed. But on MacOS, there is only one app (R.app) installed in the application folder. As a result, an error message entitled "Failed to find R executable" appears. Please make sure your R installation folder is correct. (For example: 'C:/Program Files/R/R-4.2.3')"

Full description of the error in "Steps To Reproduce"

Steps To Reproduce

Go to "DESeq2 differential expression setup"
Click on "Start DESeq2"
Get the Error message:

Traceback (most recent call last):
File "rnalysis/utils/io.py", line 1418, in run_r_script
File "rnalysis/utils/io.py", line 1482, in run_subprocess
File "subprocess.py", line 1026, in init
File "subprocess.py", line 1950, in _execute_child
FileNotFoundError: [Errno 2] No such file or directory: 'Rscript'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "rnalysis/gui/gui.py", line 4168, in finish_generic_job
File "rnalysis/gui/gui_widgets.py", line 375, in run
File "rnalysis/filtering.py", line 2882, in differential_expression_deseq2
File "rnalysis/utils/differential_expression.py", line 123, in run_deseq2_analysis
File "rnalysis/utils/differential_expression.py", line 81, in install_deseq2
File "rnalysis/utils/io.py", line 1423, in run_r_script
FileNotFoundError: Failed to find R executable. Please make sure your R installation folder is correct.
(For example: 'C:/Program Files/R/R-4.2.3')

Expected behavior

Start the DESeq2 analysis

Screenshots

How did you install RNAlysis?

Stand-alone app

RNAlysis version

3.9.2

Operating system

iOS 13.4.1

Additional context

No response

Kallisto quantification fails to execute

sRNA analysis pipeline version: 3.6.2
Python version: 3.10.9
Operating System: Windows

Description

I have used RNAlysis before, I was just trying to use the kallisto gene quantification tool for 8 paired end read fastq samplles, but when starting the quant a message error appears.

Traceback (most recent call last):
  File "rnalysis\gui\gui.py", line 3662, in finish_generic_job
  File "rnalysis\gui\gui_widgets.py", line 329, in run
  File "rnalysis\fastq.py", line 850, in kallisto_quantify_paired_end
  File "rnalysis\fastq.py", line 898, in _parse_kallisto_misc_args
  File "rnalysis\utils\io.py", line 1459, in generate_base_call
  File "rnalysis\utils\io.py", line 1400, in run_subprocess
  File "subprocess.py", line 858, in __init__
  File "subprocess.py", line 1311, in _execute_child
OSError: [WinError 193] %1 no es una aplicación Win32 válida

What could be causing the issue?

Bug Report: Translate gene IDs, FileNotFoundError

Describe the bug

Hey.

I want to translate the ensemble gene names into UniProit names but I get this error:

Traceback (most recent call last):
File "rnalysis/gui/gui.py", line 2554, in redo
File "rnalysis/gui/gui.py", line 2539, in redo
File "rnalysis/gui/gui.py", line 1970, in _apply_function_from_params
File "rnalysis/gui/gui.py", line 1356, in _apply_function_from_params
File "rnalysis/filtering.py", line 392, in translate_gene_ids
File "rnalysis/utils/io.py", line 1039, in map_gene_ids
File "rnalysis/utils/io.py", line 1250, in _get_id_abbreviation_dicts
FileNotFoundError: [Errno 2] No such file or directory: '/var/folders/6h/vt6qqj_n7s983x66mn0q_d9h0000gn/T/_MEI0jL4t9/rnalysis/utils/../data_files/uniprot_dataset_abbreviation_dict.json'

Here is the shortened file I used for this:
head.csv

Is my RNAlysis installation missing data?

Steps To Reproduce

loaded table
general
translate gene IDs

translate to UniProtKB AC/ID
translate from Ensembl

(I also tried other translate to and also auto for translate from. As far as I can see the error message is always the same)

Expected behavior

No response

Screenshots

No response

How did you install RNAlysis?

Stand-alone app

RNAlysis version

3.6.0

Operating system

MacOS 12.7

Additional context

No response

DESeq2 fails to execute

sRNA analysis pipeline version: 3.7.0
Python version:
Operating System: MacOS

Description

Hi there, I am using the stand-alone interface of RNAlysis on MacOS, I have used it with success previously. I am trying to run DESeq2 on the output table generated from kallisto, but it keeps giving me the following error after about 15 seconds of running.

Traceback (most recent call last):
File "rnalysis/gui/gui.py", line 4130, in finish_generic_job
File "rnalysis/gui/gui_widgets.py", line 375, in run
File "rnalysis/filtering.py", line 2864, in differential_expression_deseq2
File "rnalysis/utils/differential_expression.py", line 130, in run_deseq2_analysis
File "rnalysis/utils/io.py", line 1416, in run_r_script
AssertionError: R script failed to execute (return code 1).

Thanks for any help you can provide!

Bug Report: Unable to import RNAlysis into python

Describe the bug

Hi,

I am using Windows 11, Spyder IDE 5.4.3 and Python 3.11.5.

I installed RNAlysis through pip install RNAlysis[all].

However, when I try to import the package with 'from rnalysis import fastq`, I get the following error code:

Traceback (most recent call last):

Cell In[12], line 1
from rnalysis import fastq

File ~\anaconda3\Lib\site-packages\rnalysis\fastq.py:21
from rnalysis import filtering

File ~\anaconda3\Lib\site-packages\rnalysis\filtering.py:37
class Filter:

File ~\anaconda3\Lib\site-packages\rnalysis\filtering.py:452 in Filter
def find_paralogs_ensembl(self, organism: Union[Literal['auto'], str, int, Literal[get_ensembl_taxons()]] = 'auto',

File ~\anaconda3\Lib\site-packages\rnalysis\utils\param_typing.py:118 in get_ensembl_taxons
taxons = parsing.data_to_tuple(io.get_legal_ensembl_taxons())

File ~\anaconda3\Lib\site-packages\rnalysis\utils\io.py:2116 in get_legal_ensembl_taxons
results = client.run()[0]['species']

File ~\anaconda3\Lib\site-packages\rnalysis\utils\io.py:1115 in run
res = asyncio.run(self._run())

File ~\anaconda3\Lib\asyncio\runners.py:186 in run
raise RuntimeError(

RuntimeError: asyncio.run() cannot be called from a running event loop

Now when I check asyncio with pip show asyncio, it does say that I have it:

Name: asyncio
Version: 3.4.3
Summary: reference implementation of PEP 3156
Home-page: http://www.python.org/dev/peps/pep-3156/
Author: UNKNOWN
Author-email: UNKNOWN
License: UNKNOWN
Location: C:\Users\Celin\anaconda3\Lib\site-packages
Requires:
Required-by:
Note: you may need to restart the kernel to use updated packages.

It also said I needed GraphViz and add it to PATH, but I did that.

Can you help me solve this problem?

Kind Regards,

Celine

Steps To Reproduce

install RNAlysis through pip install RNAlysis[all].
import package with 'from rnalysis import fastq`

Expected behavior

I expected to just import the package and being able to use it.

Screenshots

How did you install RNAlysis?

installed via pip/Python

RNAlysis version

3.11.0

Operating system

Windows 11

Additional context

No response

GO Enrichment Analysis mouse ensembl ids mapping problem: AssertionError: Dataset 'PR' is not a valid Uniprot Dataset to map gene names/IDs from.

Describe the bug
latest RNAlysis 3.7.0, same bug on 3.6.2.
When trying to run Enrichment Analysis using Gene Ontology (GO) dataset, with my enrichment set (400 ENSMUSG Ensembl gene ids) and background set (13700 ids) of Mus musculus genes, I get this error:

Traceback (most recent call last):
File "rnalysis\gui\gui.py", line 3733, in finish_enrichment
File "rnalysis\gui\gui_widgets.py", line 329, in run
File "rnalysis\enrichment.py", line 637, in go_enrichment
File "rnalysis\utils\enrichment_runner.py", line 157, in run
File "rnalysis\utils\enrichment_runner.py", line 1061, in fetch_annotations
File "rnalysis\utils\enrichment_runner.py", line 1071, in _generate_annotation_df
File "rnalysis\utils\enrichment_runner.py", line 1129, in _translate_gene_ids
File "rnalysis\utils\io.py", line 1058, in map_gene_ids
File "rnalysis\utils\validation.py", line 178, in validate_uniprot_dataset_name
AssertionError: Dataset 'PR' is not a valid Uniprot Dataset to map gene names/IDs from. Valid Uniprot Datasets are: UniProtKB AC/ID, UniProtKB AC, UniProtKB ID, UniProtKB_to, .... # I have shortened the list.

Sometimes: Dataset 'RefSeq' is not valid Uniprot Dataset....

KEGG dataset works fine.

To Reproduce
Steps to reproduce the behavior:

Go to 'Enrichment Analysis' and load datasets, choose External dataset GO, choose organism (Mus) and gene_id_type (Ensembl), rest default.
Click on 'run'
See error

Expected behavior
KEGG dataset works fine, but not GO dataset.

Screenshots
see traceback copy

Desktop (please complete the following information):

OS: Windows 10 Pro
Version 22H2

How did you install RNAlysis?

Stand-alone app

Error in running Bowtie2

Hello Guy,
I have followed your instructions to install bowtie2 but still I'm not able to use it in RNAlysis.
I'm getting the error mentioned below :

Traceback (most recent call last):

File "rnalysis\utils\io.py", line 1479, in generate_base_call

File "rnalysis\utils\io.py", line 1420, in run_subprocess

File "subprocess.py", line 858, in init

File "subprocess.py", line 1311, in _execute_child

FileNotFoundError: [WinError 2] The system cannot find the file specified

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "rnalysis\gui\gui.py", line 3697, in finish_generic_job

File "rnalysis\gui\gui_widgets.py", line 329, in run

File "rnalysis\fastq.py", line 747, in bowtie2_align_paired_end

File "rnalysis\fastq.py", line 803, in _parse_bowtie2_misc_args

File "rnalysis\utils\io.py", line 1482, in generate_base_call

FileNotFoundError: RNAlysis could not find 'bowtie2'. Please ensure that your installation folder is correct, or add it to PATH.

I have been trying to figure out this from the past two days. Still I didn't find any solution.

Can you please help me with this?

Thank you
Regards

Bug Report: AssertionError: R script failed to execute (return code 1)

Describe the bug

Hey
I'm using RNAlysis for the first time. So please bear with me if my problem is stupid :)

I wanted to use DESeq2 differential expression on different datasets but I always get this error report:

Traceback (most recent call last):
File "rnalysis/gui/gui.py", line 3656, in finish_generic_job
File "rnalysis/gui/gui_widgets.py", line 291, in run
File "rnalysis/filtering.py", line 2747, in differential_expression_deseq2
File "rnalysis/utils/differential_expression.py", line 130, in run_deseq2_analysis
File "rnalysis/utils/io.py", line 1377, in run_r_script
AssertionError: R script failed to execute (return code 1).

I installed R and DESeq2. Is it a version problem? I'm using RNAlysis 3.6.0
I tried to install the most recent version but it won't start in contrast to 3.6.0.
I'm using macOS Monterey (12.7) on a MacBook Pro, 2019.

Thanks for any help and all the best
Michael

Steps To Reproduce

table "elegans_developmental_stages_filt50.0reads_filt50.0reads loaded

General

Run DESeq2 differential expression setup

design matrix loaded

r installation auto

output folder: disable input? checked

comparison Adult vs Embryo

Expected behavior

No response

Screenshots

No response

How did you install RNAlysis?

Stand-alone app

RNAlysis version

3.6.0

Operating system

MacOS 12.7

Additional context

No response

pyarrow.vendored.version - closing tabs or saving session

Hello,

I am using RNAlysis for the first time and am able to generate tables, plots etc. However when I go to save my session or close down some tabs/tables I keep getting errors. "ModuleNotFoundError: No module named 'pyarrow.vendored.version'"

I am not experienced generally with coding or python, I have installed pyarrow as well as pandas, but I'm not sure how to get rid of this module error, any help is appreciated.

Thank you

Incomplete Install

I installed rnalysis by following the installation instructions but it didn't install all of the files.
I am on MacOS Ventura and I am using python 3.9

PacBio sequencing and Transposons

Dear GuyTecichman

Thank you so much for develpeing this tool. it is more easer firendly.

But I coud not find the running time, because I want to run more than 100 samples (Genome size is 2.5 Gb).

Can we use this tool to analysis long reds (PacBio sequencing) and Transposons from plant genome.

with regards

windows, HPC and Ubuntu for windows installation?

Hi Team

Thank you so much for allowing this app to see light, I am hearing pretty good news about RNAlysis and can't wait to use. I asked our university server team to install it on their Linux system. But for windows as I am not used to use terminal on windows not sure if there is easier way of installing RNAlysis on windows? I installed the required software.

kallisto doesn't want to install!
I used this windows version from the link you provided

Additionally, I haven't used pip or my windows terminal before and I got this warning/error.

Thanks
M