Projects in Awesome Lists tagged with rnaseq

https://github.com/COMBINE-lab/salmon

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

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

Last synced: 17 Nov 2024

https://github.com/galaxyproject/training-material

A collection of Galaxy-related training material

chip-seq hacktoberfest materials metagenomics ngs proteomics rnaseq training tutorial usegalaxy

Last synced: 03 Nov 2024

https://github.com/sdparekh/zUMIs

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

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

Last synced: 06 Nov 2024

https://github.com/mikelove/bioc-refcard

Bioconductor cheat sheet

bioconductor bioinformatics cheatsheet compbio guide howto microarray r rnaseq

Last synced: 01 Nov 2024

https://github.com/nextflow-io/rnaseq-nf

A proof of concept of RNAseq pipeline

genomics nextflow rnaseq

Last synced: 13 Nov 2024

https://github.com/earmingol/cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

bioinformatics bulk-rna-seq cell-cell-communication cell-cell-interaction computational-biology machine-learning rna-seq rnaseq sc-rna-seq single-cell single-cell-rna-seq

Last synced: 15 Dec 2024

https://github.com/lcolladotor/derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

annotation-agnostic bioconductor derfinder r rnaseq rstats

Last synced: 18 Dec 2024

https://github.com/greenelab/rnaseq_titration_results

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

analysis bioinformatics cancer gene-expression machine-learning microarray normalization rnaseq supplement

Last synced: 13 Nov 2024

https://github.com/yyoshiaki/VIRTUS

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

cwl rnaseq virus-detection

Last synced: 23 Oct 2024

https://github.com/lieberinstitute/recount3

Explore and download data from the recount3 project

annotation-agnostic bioconductor count derfinder exon gene human illumina junction mouse r recount recount3 rnaseq rstats

Last synced: 30 Nov 2024

https://github.com/Novartis/pisces

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

bioinformatics bioinformatics-pipeline rnaseq rnaseq-pipeline salmon transcriptomics

Last synced: 26 Sep 2024

https://github.com/mikelove/alpine

Modeling and correcting fragment sequence bias for RNA-seq

bioconductor rnaseq

Last synced: 27 Oct 2024

https://github.com/mikelove/deseq2_or_edger

DESeq2 or edgeR

bioconductor deseq2 rnaseq

Last synced: 12 Oct 2024

https://github.com/crazyhottommy/pyflow-rnaseq

RNAseq pipeline based on snakemake

rnaseq snakemake

Last synced: 13 Nov 2024

https://github.com/sib-swiss/rnaseq-introduction-training

Webpage of the "Introduction to RNA-Seq: From quality control to pathway analysis - streamed" SIB course.

course rnaseq

Last synced: 28 Nov 2024

https://github.com/sydney-informatics-hub/bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts cancer genomics germline-variants indels metagenomics nextflow nextflow-pipelines ngs research-computing rnaseq snps somatic-variants sydney-informatics-hub transcriptomics variant-calling

Last synced: 21 Nov 2024

https://github.com/lieberinstitute/brainseq_phase2

BrainSeq Phase II project lead by LIBD for the BrainSeq Consortium

brainseq brainseqphase2 rnaseq rstats schizophrenia sczd

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/recount-brain

Code and analyses for the recount-brain project

human metadata public recount rnaseq rstats

Last synced: 30 Nov 2024

https://github.com/czheluo/mbsa

Multple methods for BSA Pipeline

bsa bsr fine-mapping ngs-analysis qtl-analyses rnaseq stats

Last synced: 18 Nov 2024

https://github.com/sysbiochalmers/orthomics

Collection of scripts for gene age sorting and multi-omics data mining and analysis

data-integration data-visualization de-analysis orthology proteomics rnaseq

Last synced: 03 Dec 2024

https://github.com/inab/smartrnaseqcaller

SmartRNASeqCaller is a post-processing pipeline to improve germline variant calling from RNA-Seq data

rd-connect rnaseq

Last synced: 10 Nov 2024

https://github.com/lieberinstitute/jaffelab

R package with commonly used functions by the Jaffe lab

libd rnaseq rstats

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/speaqeasy

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

hisat2 nextflow pipeline rna-seq-pipeline rnaseq rstats speaqeasy

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/libd_stem_timecourse

cell rnaseq stem timecourse

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/rnaseq-pipeline

Original version of the RNA-seq pipeline implemented in SPEAQeasy at https://github.com/LieberInstitute/SPEAQeasy.

rnaseq rstats speaqeasy

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/recount.bwtool

Fast coverage matrices from recount data using bwtool

annotation-agnostic bioconductor bwtool count r recount rnaseq rstats

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/recountworkflow

Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/

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

Last synced: 30 Nov 2024

https://github.com/datasnakes/htseq-count-cluster

A cli for running multiple qsub jobs with HTSeq's htseq-count on a cluster.

cli cluster htseq htseq-count htseq-count-cluster rnaseq sge

Last synced: 16 Nov 2024

https://github.com/datasnakes/rnaseek

A shiny app to perform single and multifactor differential analysis using DESeq2, edgeR, and limma

count-table deseq2 htseq r rna-seq rnaseq shiny shiny-apps

Last synced: 16 Nov 2024

https://github.com/lieberinstitute/recount3-docs

Documentation for all things related to `recount3`

bioconductor hg38 human mm10 mouse recount recount2 recount3 rnaseq rstats

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/qsva_brain

qSVA adapted for 2 brain regions as part of the BrainSeq Phase II project

brainseqphase2 degradation rnaseq rstats schizophrenia sczd

Last synced: 30 Nov 2024

https://github.com/r78v10a07/RNASeqWF

This code shows the validation of Differential Gene Expression Analysis from RNASeq data using as quantificator tools TPMCalculator

cwl jupyter-notebook rnaseq

Last synced: 23 Oct 2024

https://github.com/lieberinstitute/recountworkshop

Package for the recount workshop for BioC2017

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

Last synced: 30 Nov 2024

https://github.com/lieberinstitute/speaqeasy-example

Full length example for SPEAQeasy

rnaseq rstats speaqeasy

Last synced: 30 Nov 2024

https://github.com/stracquadaniolab/cubseq-nf

CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.

codon-bias codon-optimization codon-usage nextflow rnaseq transcriptomics