Top 16 rnaseq open source projects

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

✭ 22

r shell python Dockerfile machine-learning bioinformatics analysis cancer gene-expression rnaseq microarray normalization supplement

Scribe-py

Regulatory networks with Direct Information in python

✭ 28

python network velocity rnaseq causality singlecell slam-seq

DAtest

Compare different differential abundance and expression methods

✭ 34

r metagenomics rnaseq auc proteomics metabolomics microbiome false-positive-control differential-expression 16s otu marker-gene-analysis relative-abundances compare-methods differential-abundance-methods

VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

✭ 28

Common Workflow Language python shell Dockerfile rnaseq cwl virus-detection

NGI-RNAseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

✭ 50

bioinformatics rna-seq pipeline rnaseq rna-sequencing

rnaseq-nf

A proof of concept of RNAseq pipeline

✭ 44

Nextflow Makefile Dockerfile shell genomics rnaseq

pisces

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

✭ 23

python r TeX bioinformatics bioinformatics-pipeline rnaseq transcriptomics salmon rnaseq-pipeline

tximport

Import and summarize transcript-level estimates for gene-level analysis

✭ 117

r bioconductor rnaseq deseq2

rnatoy

A proof of concept RNA-Seq pipeline with Nextflow

✭ 32

Nextflow Dockerfile docker rna-seq rnaseq

alpine

Modeling and correcting fragment sequence bias for RNA-seq

✭ 25

r bioconductor rnaseq

ngs pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

✭ 40

python perl r shell snakemake pipeline panel ngs tophat gatk rnaseq fastq exome ngs-pipeline annovar snpeff

atacr

Analysing Capture Seq Count Data

✭ 14

r science data bioinformatics genomics analysis capture rnaseq atac-seq count-data

pm4ngs

Project Manager for NGS data analysis

✭ 21

python bioinformatics next-generation-sequencing rnaseq ngs-analysis ngs-pipeline cwl-workflow chipseq chipexo

viGEN

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

✭ 24

bioinformatics virus genomics rnaseq bacteria

recount

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

✭ 40

r Makefile count gene human rstats bioconductor rnaseq deseq2 illumina exon junction derfinder annotation-agnostic recount

ExpressionMatrix2

Software for exploration of gene expression data from single-cell RNA sequencing.

✭ 29

C++python c clustering rnaseq locality-sensitive-hashing single-cell

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