rna-seq-analysis

There are 5 repositories under rna-seq-analysis topic.

theislab / scarches
Reference mapping for single-cell genomics
single-cell deep-learning rna-seq-analysis data-integration batch-correction multimodal-deep-learning multiomics single-cell-genomics scrna-seq human-cell-atlas
Language:Jupyter Notebook 310
bambu
GoekeLab / bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
bambu transcript-reconstruction transcript-quantification long-reads nanopore-sequencing transcriptomics rna-seq-analysis bioconductor r nanopore rna-seq
Language:R 163
RNAlysis
GuyTeichman / RNAlysis
RNA sequencing analysis software
rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna smallrna-seq gui-application
Language:Python 119
bigomics / omicsplayground
Visual self-service analytics platform for big omics data.
omics genomics-visualization genomics rna-seq rna-seq-analysis
Language:R 113
Dragonmasterx87 / 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
3dpca 3dtsne 3dumap plotting rna-seq-analysis scrnaseq scrnaseq-data seurat seurat-objects umap
Language:R 109
MaayanLab / Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
rna-seq rna-seq-analysis pipeline notebook jupyter-notebook bioinformatics-pipeline
Language:Jupyter Notebook 100
nunofonseca / irap
integrated RNA-seq Analysis Pipeline
irap pipeline rna-seq-analysis rna-seq gene-expression transcript-quantification bulk-rna-seq single-cell-rna-seq exon-quantification differential-expression
Language:R 82
federicomarini / GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
rna-seq-data rna-seq-analysis transcriptomics r shiny transcriptome reproducible-research gui user-friendly bioconductor bioconductor-package functional-enrichment-analysis pathway-analysis gene-expression data-visualization data-exploration
Language:R 75
nellore / rail
Scalable RNA-seq analysis
rna-seq-analysis emr mapreduce alignments ipython rail-rna
Language:Python 73
broadinstitute / single_cell_portal_core
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
single-cell-genomics rna-seq-analysis human-cell-atlas
Language:Ruby 60
federicomarini / pcaExplorer
pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
principal-components rna-seq-data rna-seq-analysis r shiny transcriptome reproducible-research user-friendly bioconductor
Language:R 52
uc-bd2k / GREIN
GREIN : GEO RNA-seq Experiments Interactive Navigator
rna-seq geo bioinformatics-pipeline bioinformatics-analysis rna-seq-pipeline rna-seq-data rna-seq-analysis graphical-interface r shiny-apps gene-expression-omnibus interactive-visualizations interactive-analysis processing geo-data-processing grein gene-expression
Language:HTML 47
broadinstitute / single_cell_portal
Tutorials, workflows, and convenience scripts for Single Cell Portal
single-cell-genomics rna-seq-analysis human-cell-atlas
Language:HTML 45
govinda-kamath / clustering_on_transcript_compatibility_counts
Clustering cells from single cell RNA seq assays
paper rna-seq rna-seq-analysis single-cell-rna-seq transcript-compatibility-counts
Language:Jupyter Notebook 45
junchaoshi / sports1.1
Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
small-rna rna-seq-analysis rna-seq-mapping trna-derived-small-rna rrna-derived-small-rna mirna pirna tsrna rsrna modification trf trna-halves trna-fragment
Language:Perl 44
jumphone / SPRINT
SNP-free RNA editing Identification Toolkit
rna-seq-analysis rna-editing rna-seq rna-seq-pipeline rna-seq-mapping
Language:Python 42
jyyulab / NetBID
Data-driven Network-based Bayesian Inference of Drivers
bayesian-inference network-analysis rna-seq-analysis scrna-seq-analysis r-package
Language:R 39
pmartR / pmartR
The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data.
metabolomics-data peptides mass-spectrometry data-summarization proteins metabolites lipids rna-seq-analysis
Language:R 36
smangul1 / 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.
rna-seq-analysis t-cell-receptor circrna repeats alu immunoglobulin
Language:Shell 34
saketkc / rna-seq-snakemake
Snakemake based pipeline for RNA-Seq analysis
rna-seq-analysis snakemake pipeline bioinformatics rna-seq-snakemake
Language:R 31
nf-core / lncpipe
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
lncrna rna-seq-analysis transcriptome differential-expression nf-core nextflow workflow pipeline rna long-non-coding non-coding
Language:Nextflow 30
federicomarini / ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
differential-expression rna-seq rna-seq-analysis r shiny reproducible-research user-friendly bioconductor
Language:R 29
giuliospinozzi / arpir
Automatic RNA-Seq Pipelines with Interactive Report
rna-seq rna-seq-pipeline rna-seq-analysis report-generator automated
Language:R 25
bpucker / RNA-Seq_analysis
scripts for RNA-Seq analysis
count-table rna-seq-analysis python gff featurecounts reference-genes annotations gene-expression tpm fpkm
Language:Python 23
scGEAToolbox
jamesjcai / scGEAToolbox
scGEAToolbox: Matlab toolbox for single-cell gene expression analyses
scrna-seq workflow demo-scripts analyses dimensionality trajectory matlab-toolbox rna-seq-analysis tsne phate matlab single-cell
Language:HTML 23
iMOKA
RitchieLabIGH / iMOKA
interactive Multi Objective K-mer Analysis
singularity angular gui k-mer rna-seq-analysis data-analysis machine-learning
Language:JavaScript 23
SchulzLab / ORNA
Fast in-silico normalization algorithm for NGS data
ngstools normalization rna-seq metagenomics metagenomic-analysis rna-seq-analysis
Language:C++ 22
sunyumail93 / PipeRNAseq
A comprehensive pipeline for RNAseq data analysis
rnaseq-pipeline transcriptome-analysis bioinformatics rnaseq bioinformatics-analysis bioinformatics-pipeline gene-expression rna rna-seq-analysis rna-sequencing
Language:Shell 20
carpentries-incubator / workflows-nextflow
Workflow management with Nextflow and nf-core
lesson carpentries-incubator english pre-alpha rna-seq-analysis workflow-management bulk-rna-seq nextflow nf-core
Language:Nextflow 19
carpentries-incubator / bioc-rnaseq
Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
lesson english carpentries-incubator bioconductor pre-alpha bulk-rna-seq rna-seq-analysis r life-sciences hacktoberfest
Language:R 18
btmonier / vidger
Make rapid visualizations of RNA-seq data in R
visualization rna-seq-analysis differential-expression gene-expression data-munging r
Language:R 17
blengerich / Personalized_Regression
Personalized Regression
genomics transcriptomics rna-seq-analysis linear-regression logistic-regression personalization personalized-regression
Language:Python 15
dzhang32 / dasper
Detecting Aberrant Splicing Events from RNA-sequencing data
splicing diagnostics rare-disease rna-seq-analysis
Language:R 15
VCCRI / Ularcirc
An R-shiny app that provides backsplice and canonical splicing analysis for both circular RNA (circRNA) and parental transcripts
backsplicing circrna circular-rna rna-seq rna-seq-analysis sequencing-rna splicing-analyses splicing-visualization
Language:R 15
egaffo / CirComPara
:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
bioinformatics-pipeline bioinformatics rna-seq circrna rna-seq-data rna-seq-analysis rna-seq-pipeline gene-expression circrnas circular-rna transcriptomics circseq
Language:R 14
nasqar / deseq2shiny
a web-based R shiny application that wraps DESeq2 R package
rna-seq bulk-rna-seq rna-seq-analysis shiny shinyapps r deseq2 webapplication rshiny visualization bioinformatics
Language:R 14