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analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

ananse

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples. http://anansepy.readthedocs.io

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

annotables

R data package for annotating/converting Gene IDs

atac-seq-pipeline

ENCODE ATAC-seq pipeline

atactk

A toolkit for working with ATAC-seq data.

awesome-bioinformatics-benchmarks

A curated list of bioinformatics bench-marking papers and resources.

awesome-code-review

An "Awesome" list of code review resources - articles, papers, tools, etc

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bam2wig

Conversion of a BAM alignment to wiggle and bigwig coverage files, with flexible reporting options

bioconda-recipes

Conda recipes for the bioconda channel.

bite

BITE: BioInformatics tools for everyone

bremsc

Novel joint clustering method with scRNA-seq and CITE-seq data

bulk-rnaseq-analysis

A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.

bus_notebooks_r

R vignettes for processing BUS format single-cell RNA-seq files

cellbrowser

Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor

cellguide

🧭 Navigate single-cell RNA-seq datasets in your web browser.

cellmembrane

An R package with wrappers and pipelines for single cell RNA-seq analysis

cellranger

10x Genomics Single Cell 3' Gene Expression and VDJ Assembly

cheatsheets

Official Matplotlib cheat sheets

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

class_2021

Statistical and computational analysis of the human genome

class_2022

class_2023

dendro

Genetic Heterogeneity Profiling by Single Cell RNA Sequencing

dge_workshop_salmon_online

diamond

Accelerated BLAST compatible local sequence aligner.

diamond-1

DIseAse MODule identification algorithim