transcriptome

Star

Here are 100 public repositories matching this topic...

Language:All

Filter by language

All100 R26 Python24 HTML10 Jupyter Notebook8 Perl6 C++5 Nextflow5 C3 Shell3 Java2

Sort:Most stars

Sort options

Most stars Fewest stars Most forks Fewest forks Recently updated Least recently updated

COMBINE-lab /salmon

Star795

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

c-plus-plus bioinformatics rna-seq gene-expression rnaseq scrna-seq quantification transcriptome single-cell quasi-mapping salmon sailfish 10x single-cell-rna-seq selective-alignment rna-seq-quantification

UpdatedMay 29, 2024
C++

bcgsc /NanoSim

Star263

Nanopore sequence read simulator

simulator genome transcriptome oxford-nanopore nanopore-sequencing

UpdatedMar 2, 2025
Python

ZJUFanLab /scCATCH

Star226

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

rna-seq sequencing transcriptome transcriptomics single-cell marker-genes seurat cluster-annotation cell-markers

UpdatedMay 8, 2023
R

mortazavilab /TALON

Star141

Technology agnostic long read analysis pipeline for transcriptomes

pacbio transcriptome oxford-nanopore transcript-quantification

UpdatedJan 25, 2024
Python

greenelab /pancancer

Star120

Building classifiers using cancer transcriptomes across 33 different cancer-types

classifier machine-learning analysis tool cancer tcga gene-expression methodology transcriptome pancancer

UpdatedApr 30, 2019
Jupyter Notebook

eead-csic-compbio /get_homologues

Star113

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

annotation clustering plants genbank fasta bacteria transcriptome pangenome pangene

UpdatedMar 3, 2025
Perl

jminnier /STARTapp

Star90

The START App: R Shiny Transcriptome Analysis Resource Tool

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

UpdatedNov 11, 2020
HTML

federicomarini /GeneTonic

Star77

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

gui r 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

UpdatedMar 19, 2025
R

bcgsc /mavis

Star74

Merging, Annotation, Validation, and Illustration of Structural variants

visualization python bioinformatics genomics transcriptome structural-variation

UpdatedAug 22, 2023
Python

mortazavilab /swan_vis

Star58

A Python library to visualize and analyze long-read transcriptomes

bioinformatics long-read pacbio transcriptome oxford-nanopore pacbio-iso-seq

UpdatedMar 14, 2024
Jupyter Notebook

ksahlin /isONclust

Star58

De novo clustering of long transcript reads into genes

bioinformatics clustering transcriptome oxford-nanopore pacbio-iso-seq

UpdatedNov 4, 2021
Python

comprna /RATTLE

Star57

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

bioinformatics rna-seq nanopore genomics clustering transcriptome

UpdatedFeb 15, 2024
C++

federicomarini /pcaExplorer

Star56

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

r shiny reproducible-research bioconductor transcriptome user-friendly rna-seq-analysis principal-components rna-seq-data

UpdatedMar 7, 2025
R

enormandeau /gawn

Star43

Genome Annotation Without Nightmares

pipeline genomics genome-annotation transcriptome

UpdatedJan 24, 2025
Perl

drostlab /myTAI

Star42

Evolutionary Transcriptomics with R

gene-sets r evolution gene-expression conservation transcriptome evolutionary-transcriptomics evo-devo studies-transcriptomes biological-processes mytai expression-profiles

UpdatedMar 10, 2025
R

bcgsc /transabyss

Star34

de novo assembly of RNA-seq data using ABySS

bioinformatics rna-seq transcriptome transcriptome-assembly

UpdatedJul 21, 2023
Python

nf-core /lncpipe

Star34

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

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

UpdatedMay 9, 2024
Nextflow

cfarkas /annotate_my_genomes

Star30

A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes

rna-seq genome-annotation transcriptome transcriptome-assembly stringtie braker2

UpdatedApr 10, 2024
Nextflow

fairliereese /LR-splitpipe

Star22

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

rna-seq long-read transcriptome single-cell demultiplexing

UpdatedOct 19, 2023
Python

svm-zhang /AGOUTI

Star19

Annotated Genome Optimization Using Transcriptome Information

algorithm next-generation-sequencing genome-annotation transcriptome genome-assembly

UpdatedMay 31, 2020
Python

Improve this page

Add a description, image, and links to thetranscriptome topic page so that developers can more easily learn about it.

Curate this topic

Add this topic to your repo

To associate your repository with thetranscriptome topic, visit your repo's landing page and select "manage topics."

Learn more

Movatterモバイル変換

Navigation Menu

Search code, repositories, users, issues, pull requests...

Provide feedback

Saved searches

Use saved searches to filter your results more quickly