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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
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/saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
cell-cell-communication data-integration gene-expression intercellular-communication ligand-receptor ligand-target network-inference rna-seq single-cell-omics single-cell-rna-seq
Last synced: 02 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/suhrig/arriba
Fast and accurate gene fusion detection from RNA-Seq data
cancer fusion-gene fusion-genes gene-fusion gene-fusions rna-seq star structural-variation variant-calling virus-integration
Last synced: 08 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/uc-bd2k/GREIN
GREIN : GEO RNA-seq Experiments Interactive Navigator
bioinformatics-analysis bioinformatics-pipeline gene-expression gene-expression-omnibus geo geo-data-processing graphical-interface grein interactive-analysis interactive-visualizations processing r rna-seq rna-seq-analysis rna-seq-data rna-seq-pipeline shiny-apps
Last synced: 02 Aug 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/tallulandrews/M3Drop
human-cell-atlas rna-seq single-cell single-cell-rna-seq
Last synced: 01 Aug 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/debsin/dropClust
Version 2.1.0 released
cluster-analysis clustering genomics lsh-forest pca rna-seq singlecell
Last synced: 01 Aug 2024
https://github.com/biocorecrg/MOP2
Master of Pores 2
cdna docker nanopore nextflow pipeline rna rna-seq singularity
Last synced: 02 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/SystemsGenetics/gene-oracle
Feature extraction algorithm for genomic data
bioinformatics dataset deep-learning gene genetic-algorithm machine-learning rna-seq
Last synced: 31 Jul 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