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krumlovsinglecellworkshop2020

Course Website

krumlovtrinityworkshopjan2020

Trinity rnaseq workshop in Cesky Krumlov, Czech Republic, Jan 2020

labs

Rmd source files for the HarvardX series PH525x

lidkalee

Config files for my GitHub profile.

malfoy.github.io

matchannot

Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.

matplotlib-and-seaborn-tutorial

tutorials for easy understanding of matplotlib and seaborn commands for graph plotting

microbiome-analysis-using-r

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

minibioreactor_dataanalysis

Scripts for data analysis of plate reader experiments

miseq_analysis

ml-study-group-pl-fc

Data Available as a result of our machine learning groups pl on facebook (learning from book introduction to statistical learning)

nextflow-tutorial

Nextflow tutorial based on example by Paulo Di Tomaso and Emilio Palumbo: https://github.com/nextflow-io/rnatoy.git

ngs19

materials for #NGSchool2019 - Machine Learning for Biomedicine

ngs19_python_intro

Introduction to Python3

paper-pasp

pasta

Library to refactor python code through AST manipulation.

pastas

:spaghetti: Pastas is an open-source framework for the analysis of hydrological time series.

podstawy_pythona

power

Materiały z warsztatów "PoweR, czyli Python i R w Data Science dla początkujących"

practicalsessions

puppytails

Reads resulting from sequencing of TRAID-Seq samples were analyzed using a group of Python scripts that we call the “PuppyTails” program (extract_inserts.py, analyzeTails.py). Briefly, PuppyTails identifies sequences corresponding to the tRNA reporter, CCA end of the tRNA, and added tail in read 1. In read 2, the program identifies the random heptamer sequence, added tail sequence, and, if read length allows, the CCA end and tRNA reporter sequence. Reads were collapsed into unique ligation events using the random heptamer and then compared to identify and remove sequences resulting from PCR amplification (PCR duplicates). The number of unique times that each tail sequence is observed is counted. Tail sequences are sorted by length to calculate the nucleotide composition at each tail length and the number of tails per million heptamers (TPMH) measured for each tail length; these data are plotted as tail-o-grams. A subsequent Perl script (Total_Percent_nt_Analyses-vs1d.pl) was used to calculate the overall nucleotide composition of tails added by a given rNTase, accounting for the number of times that a tail sequence was observed.

pyconcz2018

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

r-class-igib

Introduction to R

r4ds

R for data science: a book

rbook

Source files for "Learning Statistics with R"

rdlazer

R course materials

rnaseq_pipeline

rnatoy

A proof of concept RNA-Seq pipeline with Nextflow

rosalind_problems