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20200103_genomics-data-science_jhu-course

This is the course from John Hopkin University

babelomics

bowtie

An ultrafast memory-efficient short read aligner

bowtie2

A fast and sensitive gapped read aligner

bowtie2_alignment_wrapper

a wrapper for finding alignments using bowtie2

chip-exo-guideline

This is a guideline for ChiP-exo data analysis

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

cobrapy

COBRApy is a package for constraints-based modeling of biological networks

cufflinks

exoprofiler

Analyzing transcription factor (TF) binding sites using ChIP-exo data.

google_cloud

mace

macs

MACS -- Model-based Analysis of ChIP-Seq

mgsa-bioc

Mirror of the mgsa Bioconductor package with full history in the master branch. Content of https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mgsa in the bioconductor branch.

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

rna_seq

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

sparta_linux

transcriptome-assembly-pipeline

trimmomatic

Read trimming tool for Illumina NGS data.