seandavi/awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Size: 1.35 MB - Last synced: 9 days ago - Pushed: 2 months ago - Stars: 2,943 - Forks: 926

nsalomonis/altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

Language: Python - Size: 264 MB - Last synced: 12 days ago - Pushed: almost 2 years ago - Stars: 91 - Forks: 29

federicomarini/GeneTonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Language: R - Size: 115 MB - Last synced: 22 days ago - Pushed: 29 days ago - Stars: 75 - Forks: 8

federicomarini/pcaExplorer

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

Language: R - Size: 57.4 MB - Last synced: 20 days ago - Pushed: 29 days ago - Stars: 52 - Forks: 17

federicomarini/awesome-expression-browser

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Size: 300 KB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 124 - Forks: 37

fomightez/simulated_data

A repository for code that generates various simulated data.

Language: Python - Size: 1000 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

nuno-agostinho/psichomics

Interactive R package to quantify, analyse and visualise alternative splicing

Language: R - Size: 56.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 33 - Forks: 12

GoekeLab/proActiv

Estimation of Promoter Activity from RNA-Seq data

Language: R - Size: 195 MB - Last synced: 10 days ago - Pushed: over 2 years ago - Stars: 44 - Forks: 12

uc-bd2k/GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator

Language: HTML - Size: 38.2 MB - Last synced: 10 days ago - Pushed: about 5 years ago - Stars: 47 - Forks: 19

wilkinsonlab/epigenomics_pipeline

Epigenomics workflow system for the semi-automated analysis of NGS data

Language: Jupyter Notebook - Size: 166 MB - Last synced: 2 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

knowmics-lab/RNAdetector

RNAdetector: a free user-friendly and stand-alone software for RNA-Seq data analysis

Language: JavaScript - Size: 73.6 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 8 - Forks: 8

SoniaRuiz/rytenlab-website

Website (.NET Core MVC architecture) for the RytenLab team (https://rytenlab.com/). It also contains the specification for the .NET Core REST API of the RytenLab Team (https://rytenlab.com/swagger/index.html).

Language: JavaScript - Size: 93.8 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

hbctraining/DGE_workshop 📦

Language: HTML - Size: 37.2 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 329 - Forks: 162

immunogenomics/amp_phase1_ra_viewer

🌻 View single-cell RNA-seq and mass cytometry data in synovial tissues from patients with RA or OA.

Language: R - Size: 1.19 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 3 - Forks: 2

sohilsshah91/nyhais-tcga-series-kmeans

Language: Jupyter Notebook - Size: 23.3 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

sivkri/miRNASeq-DE-Analysis-QC

Performing RNA-Seq data analysis and quality control using DESeq2 in R.

Language: R - Size: 110 KB - Last synced: 7 months ago - Pushed: 12 months ago - Stars: 1 - Forks: 0

adeschen/SignatureHeatmap

R package to create heatmaps using signature gene list and transcriptomic data

Language: R - Size: 1.94 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

MG-RAST/myM5NR

M5NRv2 -- non-redundant protein and rRNA database integration

Language: Perl - Size: 10.8 MB - Last synced: 2 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 3

kjohnsen/MMAPPR2data

Sample Data for MMAPPR2

Language: R - Size: 629 KB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 1

kevincjnixon/BinfTools

Useful R functions for Multi-omics analyses

Language: R - Size: 5.55 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 2

mchialva/RNA2M

Scripts used to analyze tomato meta-transcriptome from short-read host RNA-seq data in Chialva et al. (2020)

Language: R - Size: 2.95 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

egaffo/CirComPara

:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

Language: R - Size: 16 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 14 - Forks: 11

niqolla/ieo_RNAseq_project

eproduciton of a publication regarding gene expression in different phases of lactation in humans

Language: TeX - Size: 22.6 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

hbctraining/Intro-to-R-with-DGE 📦

Language: R - Size: 39.5 MB - Last synced: over 1 year ago - Pushed: about 3 years ago - Stars: 54 - Forks: 43

williamjeong2/snakemake_RNA-seq

A repository for RNA-seq workflow

Language: R - Size: 12.9 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

arfesta/Breeding-Value-Prediction

Predicting NCSU Coastal Breeding Values using RNA Seq data

Language: HTML - Size: 1.15 GB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

theislab/MetaMap

The code and analyses accompanying the manuscript “MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data”.

Language: HTML - Size: 10.9 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 11 - Forks: 8

sing-group/dewe

DEWE (Differential Expression Workflow Executor) is an open source application for easily executing Differential Expression analyses in RNA-Seq data.

Language: Java - Size: 1.38 MB - Last synced: over 1 year ago - Pushed: over 5 years ago - Stars: 3 - Forks: 0

Transipedia/dekupl

Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.

Size: 47.6 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 12 - Forks: 2

bissessk/RNA-seq-Analysis-of-Control-and-NRDE2-depleted-Breast-Cancer-Cells

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

Language: Shell - Size: 418 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

jacobwindsor/tmerge Fork of guigolab/tmerge

Build highly accurate transcripts from long-read RNA data

Language: Python - Size: 1.17 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

keslingmj/RNASeq

Analyses of RNA-Seq Data

Language: CSS - Size: 44.3 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

tAndreani/RNAseQTL

Collection of scripts to map eQTL with RNAseq Data and Genotype by Sequencing

Language: R - Size: 17.6 KB - Last synced: over 1 year ago - Pushed: about 5 years ago - Stars: 3 - Forks: 0