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Projects in Awesome Lists tagged with rna-seq

A curated list of projects in awesome lists tagged with rna-seq .

https://github.com/crazyhottommy/RNA-seq-analysis

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Last synced: 02 Aug 2024

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: 03 Aug 2024

https://github.com/theislab/single-cell-best-practices

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

book rna-seq single-cell tutorial

Last synced: 02 Aug 2024

https://github.com/deeptools/deepTools

Tools to process and analyze deep sequencing data.

bioinformatics chip-seq genomics ngs python rna-seq

Last synced: 02 Aug 2024

https://github.com/pachterlab/kallisto

Near-optimal RNA-Seq quantification

kallisto pseudoalignment rna-seq

Last synced: 02 Aug 2024

https://github.com/owkin/PyDESeq2

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

bioinformatics differential-expression python rna-seq transcriptomics

Last synced: 03 Aug 2024

https://github.com/maxplanck-ie/snakepipes

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

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

Last synced: 03 Aug 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: 01 Aug 2024

https://github.com/dtm2451/dittoSeq

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

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

Last synced: 02 Aug 2024

https://github.com/dtm2451/DittoSeq

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

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

Last synced: 01 Aug 2024

https://github.com/COMBINE-lab/alevin-fry

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

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

Last synced: 02 Aug 2024

https://github.com/vanheeringen-lab/seq2science

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.

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

Last synced: 03 Aug 2024

https://github.com/GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

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

Last synced: 02 Aug 2024

https://github.com/GoekeLab/bambu

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

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

Last synced: 02 Aug 2024

https://github.com/bigomics/omicsplayground

Visual self-service analytics platform for big omics data.

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

Last synced: 13 Aug 2024

https://github.com/bvieth/powsimR

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.

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

Last synced: 03 Aug 2024

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

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.

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

Last synced: 01 Aug 2024

https://github.com/jminnier/STARTapp

The START App: R Shiny Transcriptome Analysis Resource Tool

bioinformatics genome-biology r rna-seq shiny shiny-apps transcriptome visualization

Last synced: 02 Aug 2024

https://github.com/bcgsc/RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads

bioinformatics-tool bulk-rna-seq denovo-assembly nanopore-sequencing pacbio-sequencing rna-seq single-cell-rna-seq

Last synced: 02 Aug 2024

https://github.com/calico/scnym

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

adversarial-training rna-seq semi-supervised single-cell single-cell-genomics

Last synced: 08 Aug 2024

https://github.com/GfellerLab/EPIC

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

bulk-data cancer-cells cell-type gene-expression rna-seq

Last synced: 03 Aug 2024

https://github.com/comprna/RATTLE

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

bioinformatics clustering genomics nanopore rna-seq transcriptome

Last synced: 02 Aug 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: 02 Aug 2024

https://github.com/Novartis/cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

dataviz h5ad rna-seq scientific scrna-seq transcriptomics visualization

Last synced: 26 Sep 2024

https://github.com/swsoyee/TCC-GUI

📊 Graphical User Interface for TCC package

bioinformatics gui rna-seq shiny tcc

Last synced: 13 Aug 2024

https://github.com/bioinformatics-core-shared-training/ngs-in-bioc

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

bioconductor ngs rna-seq training

Last synced: 01 Aug 2024

https://github.com/t-neumann/slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity

bioinformatics computational-biology docker-image pypi quant-seq rna-seq slamseq transcription

Last synced: 27 Sep 2024

https://github.com/ElementoLab/scTCRseq

Processing of single cell RNAseq data for the recovery of TCRs in python

python rna-seq single-cell-rna-seq

Last synced: 01 Aug 2024

https://github.com/Bohdan-Khomtchouk/HeatmapGenerator

Cross-platform GUI desktop application for making biological heatmaps

c-plus-plus computational-biology gui-application heatmap lightweight microarray opengl r-programming rna-seq

Last synced: 02 Aug 2024

https://github.com/darwinawardwinner/cd4-csaw

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

bioconductor bioinformatics-pipeline chip-seq r reproducible-research rna-seq

Last synced: 02 Oct 2024

https://github.com/yjzhang/uncurl_python

UNCURL is a tool for single cell RNA-seq data analysis.

bioinformatics rna-seq single-cell

Last synced: 01 Aug 2024

https://github.com/nasqar/deseq2shiny

a web-based R shiny application that wraps DESeq2 R package

bioinformatics bulk-rna-seq deseq2 r rna-seq rna-seq-analysis rshiny shiny shinyapps visualization webapplication

Last synced: 13 Aug 2024

https://github.com/runsheng/trackcluster

An analysis pipeline for Nanopore direct-RNA sequencing

bioinformatics longread nanopore rna-seq

Last synced: 02 Aug 2024

https://github.com/igsr/igsr_analysis

This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data

jupyter-notebook nextflow-pipelines perl pipelines python rna-seq snp-data snp-genotyping

Last synced: 28 Sep 2024

https://github.com/unkindpartition/bamcc

bamcc — split SAM/BAM files into connected components

alignment bioinformatics biology dna rna rna-seq

Last synced: 02 Oct 2024

https://github.com/youssefayachii/hicdataanalysis

Using chromatin-chromatin interaction scores generated by the Capture Hi-C technology, I developed this R code during my six week internship in the Spicuglia lab, part of the INSERM institute (TAGC) related to the Aix-Marseille University, France, in order to identify the DNA interactions happening between different regions, specifically the interaction of the OAS3 Epromoter with its target promoters OAS1 and OAS2, before and after IFN alpha stress stimulation and then to figure out the changes of the 3D chromatin organization upon this stress stimulation.

3c chromatin genetics hic oas oas3 rna rna-seq

Last synced: 30 Sep 2024

https://github.com/art-egorov/svist4get

A simple visualisation tool for genomic tracks from sequencing experiments.

bioinformatics ngs rna-seq visualisation

Last synced: 04 Aug 2024

https://xwanglabthu.github.io/ARIC/

Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

deconvolution methylation rna-seq

Last synced: 02 Aug 2024