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bioinfosummer

Tutorial for AMSI BioInfoSummer 2018

checkin

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

chipseeker

:dart: ChIP peak Annotation, Comparison and Visualization

circlize

Circular visualization in R

clash

A rule-based tunnel in Go.

copilot

Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.

dask-tutorial

Dask tutorial

deeplncrna

dellachiara_et_al_2021

epinano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads

exomepeak

Analysis of RNA epitranscriptome sequencing data with affinity-based shotgun sequencing approach

exomepeak2

Bias aware peak calling and quantification for MeRIP-Seq

galaxy-rna-workbench

Galaxy RNA workbench

genomepy

genes and genomes at your fingertips

geo

hocnnlb

It is a deep learning method used for predicting the RBP binding sites on lncRNA chains.

intro-to-rnaseq-hpc-o2

This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster

ionmf

Integrative orthogonal non-negative matrix factorization

johnyazz

data analysis

kallisto

Near-optimal RNA-Seq quantification

m6a-seq_analysis_workflow

A pipeline to process m6A-seq data and down stream analysis.

m6amethylation

m(6)A methylation analysis

macs

MACS -- Model-based Analysis of ChIP-Seq

mazter_mine

An R program to calculate cleavage efficiency in MAZTER-seq derived data

merip_reanalysis_scripts

Scripts for paper entitled "Limits in the detection of m6A changes using MeRIP/m6A-seq

merip_seq_pipline

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

nanopolish

Signal-level algorithms for MinION data