Topic: rna-seq Goto Github

Some thing interesting about rna-seq

👇 Here are 1090 public repositories matching this topic...

ablab / isoquant

rna-seq,Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Organization: ablab

ngs transcriptomics pacbio nanopore bioinformatics rna-seq

agitter / single-cell-pseudotime

rna-seq,An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

User: agitter

single-cell rna-seq bioinformatics pseudotime-algorithms

bigomics / omicsplayground

rna-seq,Visual self-service analytics platform for big omics data.

Organization: bigomics

Home Page: http://www.bigomics.ch

omics genomics-visualization genomics rna-seq rna-seq-analysis

broadinstitute / wot

rna-seq,A software package for analyzing snapshots of developmental processes

Organization: broadinstitute

Home Page: https://broadinstitute.github.io/wot/

single-cell rna-seq time-series trajectory optimal-transport

rna-seq,Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

User: bvieth

Home Page: https://bvieth.github.io/powsimR/

gene-expression single-cell rna-seq simulation-framework simulation power experimental-design power-analysis r

combine-lab / alevin-fry

rna-seq,🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Organization: combine-lab

Home Page: https://alevin-fry.readthedocs.io

single-cell rust transcriptomics rna-seq single-cell-rna-seq quantification 10x

combine-lab / salmon

rna-seq,🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Organization: combine-lab

Home Page: https://combine-lab.github.io/salmon

quasi-mapping bioinformatics rna-seq rnaseq salmon quantification sailfish c-plus-plus gene-expression scrna-seq

crazyhottommy / rna-seq-analysis

rna-seq,RNAseq analysis notes from Ming Tang

User: crazyhottommy

rna-seq snakemake

crg-cnag / callings-nf

rna-seq,GATK RNA-Seq Variant Calling in Nextflow

Organization: crg-cnag

nextflow ngs variant-calling rna-seq gatk bioinformatics genomics

csoneson / armor

rna-seq,Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

User: csoneson

rna-seq workflow

deeptools / deeptools

rna-seq,Tools to process and analyze deep sequencing data.

Organization: deeptools

python bioinformatics genomics ngs rna-seq chip-seq

dtm2451 / dittoseq

rna-seq,Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

User: dtm2451

rna-seq single-cell single-cell-rna-seq visualization color-blindness color-blind

gagneurlab / drop

rna-seq,Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Organization: gagneurlab

genetic-diagnosis pipeline rna-seq

getzlab / rnaseqc

rna-seq,Fast, efficient RNA-Seq metrics for quality control and process optimization

Organization: getzlab

rnaseq rna-seq bioinformatics

goekelab / bambu

rna-seq,Reference-guided transcript discovery and quantification for long read RNA-Seq data

Organization: goekelab

bambu transcript-reconstruction transcript-quantification long-reads nanopore-sequencing transcriptomics rna-seq-analysis bioconductor r nanopore

goekelab / bioinformatics-workflows

rna-seq,minimal example implementations for bioinformatics workflow managers

Organization: goekelab

bioinformatics workflow-management bioinformatics-workflows pipeline rna-seq workflow

goekelab / xpore

rna-seq,Identification of differential RNA modifications from nanopore direct RNA sequencing

Organization: goekelab

Home Page: https://xpore.readthedocs.io/

rna modification transcriptomics machine-learning genomics nanopore-sequencing rna-seq rna-modifications nanopore python

guma44 / geoparse

rna-seq,Python library to access Gene Expression Omnibus Database (GEO)

User: guma44

geo-database high-throughput-sequencing htseq microarray bioinformatics rna-sequencing rna-seq

guyteichman / rnalysis

rna-seq,RNA sequencing analysis software

User: guyteichman

Home Page: https://guyteichman.github.io/RNAlysis

rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna

harbourlab / spark

rna-seq,Publication quality NGS track plotting

User: harbourlab

bedgraph-files chip-seq plotting ngs ngs-analysis rna-seq igv

kanaverse / kana

rna-seq,Single cell analysis in the browser

Organization: kanaverse

Home Page: https://kanaverse.org/kana/

single-cell interactive-visualizations exploratory-data-analysis webassembly rna-seq cite-seq bioinformatics interactive-analysis

kpatel427 / youtubetutorials

rna-seq,

User: kpatel427

bioinformatics bioinformatics-analysis rna-seq single-cell tutorials youtube

maayanlab / biojupies

rna-seq,Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

Organization: maayanlab

Home Page: http://biojupies.cloud

bioinformatics systems-biology jupyter rna-seq pipeline notebook cloud dcppc

maayanlab / zika-rnaseq-pipeline

rna-seq,An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

Organization: maayanlab

Home Page: http://bit.ly/2g4hCe7

rna-seq rna-seq-analysis pipeline notebook jupyter-notebook bioinformatics-pipeline

maxplanck-ie / snakepipes

rna-seq,Customizable workflows based on snakemake and python for the analysis of NGS data

Organization: maxplanck-ie

Home Page: http://snakepipes.readthedocs.io

ngs rna-seq chip-seq workflow atac-seq hi-c bisulfite-sequencing snakemake

milaboratory / mixcr

rna-seq,MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

Organization: milaboratory

Home Page: https://mixcr.com

bioinformatics immunology antibody t-cell-receptor t-cell rep-seq 10x rna-seq sequencing single-cell

nanoporetech / pipeline-transcriptome-de

rna-seq,Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

Organization: nanoporetech

rna-seq cdna differential-gene-expression differential-transcript-usage nanopore

ncbi / tpmcalculator

rna-seq,TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

Organization: ncbi

ngs rna-seq tpm

ndaniel / fusioncatcher

rna-seq,Finder of Somatic Fusion Genes in RNA-seq data

User: ndaniel

rna-seq fusion-genes somatic-fusion-genes

nf-core / rnafusion

rna-seq,RNA-seq analysis pipeline for detection of gene-fusions

Organization: nf-core

Home Page: https://nf-co.re/rnafusion

nf-core nextflow workflow rna-seq rna pipeline fusion-genes fusion gene-fusion

nf-core / rnaseq

rna-seq,RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Organization: nf-core

Home Page: https://nf-co.re/rnaseq

nf-core nextflow workflow rna-seq rna pipeline

nf-core / scrnaseq

rna-seq,A single-cell RNAseq pipeline for 10X genomics data

Organization: nf-core

Home Page: https://nf-co.re/scrnaseq

nf-core nextflow workflow pipeline 10x-genomics 10xgenomics alevin bustools cellranger kallisto

owkin / pydeseq2

rna-seq,A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Organization: owkin

Home Page: https://pydeseq2.readthedocs.io/en/latest/

bioinformatics differential-expression python rna-seq transcriptomics

pachterlab / kallisto

rna-seq,Near-optimal RNA-Seq quantification

Organization: pachterlab

Home Page: https://pachterlab.github.io/kallisto

kallisto rna-seq pseudoalignment

pachterlab / kallistobustools

rna-seq,kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Organization: pachterlab

Home Page: https://kallistobus.tools/

single-cell rna-seq kallisto bustools

pachterlab / sleuth

rna-seq,Differential analysis of RNA-Seq

Organization: pachterlab

Home Page: http://pachterlab.github.io/sleuth

rna-seq

rnabioco / clustifyr

rna-seq,Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets

Organization: rnabioco

Home Page: https://rnabioco.github.io/clustifyr/

assign-identities clusters marker-genes rna-seq single-cell-rna-seq

saeyslab / nichenetr

rna-seq,NicheNet: predict active ligand-target links between interacting cells

Organization: saeyslab

single-cell-omics intercellular-communication ligand-receptor ligand-target data-integration single-cell-rna-seq rna-seq gene-expression network-inference cell-cell-communication

scrna-tools / scrna-tools

rna-seq,Table of software for the analysis of single-cell RNA-seq data.

Organization: scrna-tools

Home Page: https://www.scrna-tools.org

single-cell rna-seq scrna-seq single-cell-rna-seq tools database software

sdparekh / zumis

rna-seq,zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

User: sdparekh

rnaseq rna-seq single-cell umi expression barcodes fastq dge pipeline

sequana / sequana

rna-seq,Sequana: a set of Snakemake NGS pipelines

Organization: sequana

Home Page: http://sequana.readthedocs.io

ngs variant-calling taxonomy de-novo pacbio sequanix snakemake coverage rna-seq

suhrig / arriba

rna-seq,Fast and accurate gene fusion detection from RNA-Seq data

User: suhrig

gene-fusions rna-seq cancer gene-fusion fusion-gene fusion-genes variant-calling structural-variation star virus-integration

tallulandrews / scrnaseqpipeline

rna-seq,

User: tallulandrews

single-cell-rna-seq single-cell rna-seq

theislab / single-cell-best-practices

rna-seq,https://www.sc-best-practices.org

Organization: theislab

Home Page: https://www.sc-best-practices.org

book rna-seq single-cell tutorial

timbitz / whippet.jl

rna-seq,Lightweight and Fast; RNA-seq quantification at the event-level

User: timbitz

rna-seq alternative-splicing

twbattaglia / rnaseq-workflow

rna-seq,A repository for setting up a RNAseq workflow

User: twbattaglia

bioinformatics rna-seq workflow pipeline genes sequencing science

vanheeringen-lab / seq2science

rna-seq,Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Organization: vanheeringen-lab

Home Page: https://vanheeringen-lab.github.io/seq2science

snakemake bioinformatics bioinformatics-pipeline atac-seq rna-seq chip-seq reproducible-research ngs pipeline sra