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Top 16 rna-seq-analysis open source projects

Reference mapping for single-cell genomics

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Jupyter Notebook python deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas

vidger

Make rapid visualizations of RNA-seq data in R

✭ 19

r visualization gene-expression rna-seq-analysis differential-expression data-munging

ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

✭ 24

r rna-seq shiny reproducible-research bioconductor user-friendly rna-seq-analysis differential-expression

NetBID

Data-driven Network-based Bayesian Inference of Drivers

✭ 21

r bayesian-inference r-package network-analysis rna-seq-analysis scrna-seq-analysis

rop

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.

✭ 35

shell python repeats t-cell-receptor alu rna-seq-analysis circrna immunoglobulin

sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs

✭ 35

perl r modification rna-seq-analysis mirna tsrna trf trna-derived-small-rna trna-halves small-rna rna-seq-mapping rrna-derived-small-rna pirna rsrna trna-fragment

iMOKA

interactive Multi Objective K-mer Analysis

✭ 19

javascript C++typescript HTML c python machine-learning gui angular singularity data-analysis k-mer rna-seq-analysis

GeneTonic

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

✭ 66

r gui shiny reproducible-research gene-expression data-visualization bioconductor transcriptome user-friendly data-exploration transcriptomics rna-seq-analysis pathway-analysis rna-seq-data bioconductor-package functional-enrichment-analysis

single cell portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

✭ 41

HTML python wdl r Jupyter Notebook Dockerfile rna-seq-analysis single-cell-genomics human-cell-atlas

Interactive-3D-Plotting-in-Seurat-3.0.0

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

✭ 80

r plotting rna-seq-analysis umap scrnaseq seurat 3dtsne 3dpca 3dumap scrnaseq-data seurat-objects

GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator

✭ 40

HTML r rna-seq geo graphical-interface gene-expression bioinformatics-pipeline interactive-analysis shiny-apps rna-seq-analysis rna-seq-data interactive-visualizations bioinformatics-analysis gene-expression-omnibus rna-seq-pipeline geo-data-processing grein

rail

Scalable RNA-seq analysis

✭ 74

python Mathematica java shell r emr ipython alignments mapreduce rna-seq-analysis rail-rna

scGEAToolbox

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

✭ 15

HTML matlab workflow scrna-seq analyses rna-seq-analysis tsne matlab-toolbox trajectory dimensionality phate demo-scripts

rna-seq-snakemake

Snakemake based pipeline for RNA-Seq analysis

✭ 29

r python PowerBuilder shell bioinformatics snakemake pipeline rna-seq-analysis rna-seq-snakemake

ORNA

Fast in-silico normalization algorithm for NGS data

✭ 21

C++CMake shell rna-seq metagenomics rna-seq-analysis ngstools normalization metagenomic-analysis

lncpipe

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

✭ 24

workflow pipeline rna transcriptome rna-seq-analysis differential-expression lncrna non-coding nf-core long-non-coding

1-16 of 16 rna-seq-analysis projects