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rna-seq

Here are 928 public repositories matching this topic...

crazyhottommy / RNA-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Updated Nov 15, 2021
Python

COMBINE-lab / salmon

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

c-plus-plus bioinformatics rna-seq gene-expression rnaseq scrna-seq quantification transcriptome single-cell quasi-mapping salmon sailfish 10x single-cell-rna-seq selective-alignment rna-seq-quantification

Updated Nov 29, 2022
C++

deeptools / deepTools

Tools to process and analyze deep sequencing data.

python bioinformatics rna-seq genomics ngs chip-seq

Updated Nov 28, 2022
Python

nf-core / rnaseq

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

workflow rna-seq pipeline nextflow rna nf-core

Updated Nov 23, 2022
Nextflow

pachterlab / kallisto

Near-optimal RNA-Seq quantification

rna-seq kallisto pseudoalignment

Updated Oct 12, 2022
C

agitter / single-cell-pseudotime

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

bioinformatics rna-seq single-cell pseudotime-algorithms

Updated Nov 30, 2022

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

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

Updated Dec 2, 2022
Python

saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells

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

Updated Nov 9, 2022
R

twbattaglia / RNAseq-workflow

A repository for setting up a RNAseq workflow

science workflow bioinformatics rna-seq pipeline sequencing genes

Updated Apr 10, 2017
R

pachterlab / sleuth

Differential analysis of RNA-Seq

Updated Nov 14, 2022
R

scRNA-tools / scRNA-tools

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

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

Updated Dec 5, 2022
R

sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

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

Updated May 10, 2022
R

milaboratory / mixcr

MiXCR is a universal software for fast and accurate extraction and downstream analysis of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

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

Updated Dec 5, 2022
Java

suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data

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

Updated Jun 17, 2022
C++

csoneson / ARMOR

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

workflow rna-seq

Updated Oct 21, 2022
R

ZJUFanLab / scCATCH

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

rna-seq sequencing transcriptome transcriptomics single-cell marker-genes seurat cluster-annotation cell-markers

Updated Sep 14, 2022
R

velocyto-team / velocyto.py

RNA velocity estimation in Python

rna-seq single-cell rna-velocity-estimation

Updated Feb 19, 2020
Python

theislab / single-cell-best-practices

This project is work in progress! https://www.sc-best-practices.org

tutorial rna-seq book single-cell

Updated Dec 1, 2022
Jupyter Notebook

dtm2451 / dittoSeq

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

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

Updated Nov 3, 2022
R

sequana / sequana

Sequana: a set of Snakemake NGS pipelines

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

Updated Nov 21, 2022
Jupyter Notebook

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