GitHub topics: transcriptomics

Repositories

spacetx/starfish

starfish: unified pipelines for image-based transcriptomics

Language: Python - Size: 114 MB - Last synced at: about 5 hours ago - Pushed at: about 6 hours ago - Stars: 232 - Forks: 70

SML-CompBio/OncoMark

A deep learning tool designed to predict Cancer Hallmark activities from tumor biopsy samples.

Language: Jupyter Notebook - Size: 11.3 MB - Last synced at: about 7 hours ago - Pushed at: about 8 hours ago - Stars: 0 - Forks: 0

cran-task-views/Omics

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Size: 77.1 KB - Last synced at: about 14 hours ago - Pushed at: about 15 hours ago - Stars: 18 - Forks: 5

TianyiFranklinWang/MIRROR

MIRROR: Multi-Modal Pathological Self-Supervised Representation Learning via Modality Alignment and Retention

Language: Python - Size: 8.12 MB - Last synced at: about 24 hours ago - Pushed at: 1 day ago - Stars: 8 - Forks: 0

scverse/scanpy

Single-cell analysis in Python. Scales to >100M cells.

Language: Python - Size: 41 MB - Last synced at: 1 day ago - Pushed at: 3 days ago - Stars: 2,082 - Forks: 629

CohenLabUGA/SAB_isolates

Language: Jupyter Notebook - Size: 233 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

federicomarini/GeneTonic

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

Language: R - Size: 121 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 78 - Forks: 10

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 145 MB - Last synced at: about 6 hours ago - Pushed at: 3 days ago - Stars: 33 - Forks: 9

PejLab/Pantry

Pan-transcriptomic phenotyping

Language: Python - Size: 14.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 17 - Forks: 0

bioinfodlsu/regulated-cell-death-playground

Collection of analysis scripts and notebooks related to regulated cell death

Language: HTML - Size: 91.6 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

pachterlab/gget

🧬 gget enables efficient querying of genomic reference databases

Language: Python - Size: 328 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1,020 - Forks: 77

GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.

Language: TypeScript - Size: 17.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

nf-core/spatialvi

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Language: Nextflow - Size: 7.02 MB - Last synced at: about 13 hours ago - Pushed at: about 14 hours ago - Stars: 62 - Forks: 23

number-25/rich_directRNA

Nanopore directRNA (hopefully cDNA too ;)) workflow with many transcript reconstruction alternatives

Language: HTML - Size: 7.73 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

GuyTeichman/RNAlysis

Analyze your RNA sequencing data without writing a single line of code

Language: Python - Size: 795 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 133 - Forks: 13

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.

Language: Python - Size: 203 KB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 64 - Forks: 34

marvinquiet/SpaDOT

Optimal transport modeling uncovers spatial domain dynamics in spatiotemporal transcriptomics

Language: Python - Size: 2.78 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

keller-mark/awesome-biological-visualizations

A list of web-based interactive biological data visualizations.

Size: 141 KB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 194 - Forks: 17

weylz/captureTCNE

A tailored identification framework to depict the landscape of transcribed conserved non-coding elements (TCNEs)

Language: Shell - Size: 188 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 3 - Forks: 0

guigolab/LyRic

Long RNA-seq analysis workflow

Language: Python - Size: 76.3 MB - Last synced at: 6 days ago - Pushed at: 5 months ago - Stars: 17 - Forks: 4

microbiomedata/metaT

Metatranscriptomics workflow

Language: WDL - Size: 22.2 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 4 - Forks: 2

ToruOkadaOi/scRNA_seq_analysis

Cross-platform single-cell analysis stack: R + Python + Docker + Jupyter

Language: Jupyter Notebook - Size: 100 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

owkin/fedpydeseq2

A federated implementation of PyDESeq2, based on Substra.

Language: Python - Size: 2.22 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 11 - Forks: 0

owkin/PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Language: Python - Size: 1.37 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 645 - Forks: 74

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.59 GB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 262 - Forks: 323

aertslab/pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

Language: Python - Size: 34.7 MB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 500 - Forks: 190

obophenotype/cell-ontology

An ontology of cell types

Language: Makefile - Size: 399 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 169 - Forks: 53

theislab/scgen

Single cell perturbation prediction

Language: Python - Size: 69.3 MB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 292 - Forks: 59

scverse/anndata

Annotated data.

Language: Python - Size: 5.62 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 621 - Forks: 164

michael-nakai/isopod

An R package to simulate and detect differential transcript usage in transcript-level single-cell datasets.

Language: R - Size: 596 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 4 - Forks: 0

ablab/IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Language: Python - Size: 19.7 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 164 - Forks: 15

mcrewcow/Yizhen_microglia

collab | DFC

Language: Jupyter Notebook - Size: 4.85 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 1

bpucker/Overview

Overview of repositories associated with @bpucker & @PuckerLab. This covers science communication projects, the developed bioinformatics tools, teaching activities, and project specific repositories.

Size: 171 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 0

bpucker/teaching

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

Size: 354 MB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 51 - Forks: 9

bpucker/Boas_Pucker

Homepage of Boas Pucker listing publications and professional activities

Size: 141 KB - Last synced at: 11 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 0

GoekeLab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Language: R - Size: 549 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 207 - Forks: 24

markziemann/dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Language: Shell - Size: 56 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 40 - Forks: 7

CogDisResLab/drugfindR

Repository holding the code for the drugfindR R package

Language: R - Size: 7.13 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 8 - Forks: 3

carlocolantuoni/NeocortexDevelopment_Sonthalia2024

Repository for analyses performed in "A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development" (doi.org/10.1101/2024.02.26.581612)

Size: 31.3 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

aljpetri/isONclust3

De novo clustering of long transcript reads into genes

Language: Rust - Size: 9.75 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 7 - Forks: 1

j-andrews7/halfBaked

Half-baked convenience functions for common 'omics analyses.

Language: R - Size: 24.2 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

integrativebioinformatics/LongNonCoder

A Nextflow pipeline for long non-coding RNAs discovery from long-read RNA-seq

Size: 0 Bytes - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0

plasslab/SCALPEL

Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.

Language: R - Size: 406 KB - Last synced at: about 18 hours ago - Pushed at: 15 days ago - Stars: 9 - Forks: 1

jarnokoetsier/OrganoidAnalysis

Multi-Omics Characterization of Developing Forebrain Organoids Unravels the Dynamic Molecular Events of Rett Syndrome Pathogenesis

Language: R - Size: 4.35 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 1

KalinNonchev/azimuthpy

Annotate your single-cell data using Azimuth in python.

Language: Jupyter Notebook - Size: 29.3 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

miastay/gedit3

The Gene Expression Deconvolution Interactive Tool

Language: Svelte - Size: 147 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0

NIGMS/Transcriptome-Assembly-Refinement-and-Applications

In this module, you will learn how to use a Nextflow pipeline to assemble and annotate a novel transcriptome using RNA-seq data

Language: Jupyter Notebook - Size: 5.78 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 4

ZJUFanLab/scCATCH

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

Language: R - Size: 52 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 227 - Forks: 36

theislab/DRVI

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Language: Python - Size: 14 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 41 - Forks: 3

ciccalab/Kandinsky

Language: HTML - Size: 49.1 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 0 - Forks: 0

GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

Language: Python - Size: 5 MB - Last synced at: 6 days ago - Pushed at: 6 months ago - Stars: 148 - Forks: 23

alaa2133/Cobra

[SIGGRAPH 2025] Official code of the paper "Cobra: Efficient Line Art COlorization with BRoAder References"

Language: Python - Size: 30.3 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 1

UK-SBCoA-EbbertLab/RNApysoforms

A Python adaptation of ggtranscript with similar functionality, using Plotly and Polars for fast and interactive RNA isoform visualizations.

Language: Jupyter Notebook - Size: 11.7 MB - Last synced at: 19 days ago - Pushed at: 20 days ago - Stars: 4 - Forks: 0

epigen/macrophage-regulation

Integrated time series analysis and high-content CRISPR screening delineates the dynamics of macrophage immune regulation

Language: Jupyter Notebook - Size: 29.1 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 3 - Forks: 0

arc85/celltalker 📦

Inference of cell-cell communication from single-cell RNAseq data

Language: R - Size: 11.1 MB - Last synced at: 12 days ago - Pushed at: 21 days ago - Stars: 48 - Forks: 20

saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

Language: Python - Size: 83.1 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 192 - Forks: 28

nf-core/tfactivity

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

Language: Nextflow - Size: 7.32 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 12 - Forks: 4

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.

Language: Rust - Size: 4.32 MB - Last synced at: 14 days ago - Pushed at: 2 months ago - Stars: 182 - Forks: 16

aditya19991010/single_cell_transcriptomics

This repository contains a comprehensive single-cell RNA sequencing (scRNA-seq) analysis workflow of Peripheral Blood Mononuclear Cells (PBMCs) using the Seurat package in R

Language: R - Size: 4.48 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 1 - Forks: 0

AllenInstitute/scrattch

Single cell RNA-seq analysis for transcriptomic type characterization

Language: R - Size: 97.3 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 36 - Forks: 3

benfulcher/AllenSDK

Workflow for retrieving spatial gene-expression data from the Allen Institute's Mouse Brain Atlas

Language: MATLAB - Size: 44.9 KB - Last synced at: about 2 hours ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 3

cajigas/granulifera_selection

This project studies the evolution of color polymorphism in the granular poison frog Oophaga granulifera

Language: Shell - Size: 116 KB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 0

PavlidisLab/rnaseq-pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Language: Shell - Size: 43.5 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 24 - Forks: 5

benben-miao/TOmicsVis

Transcriptomics Visualization R package.

Language: R - Size: 198 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 71 - Forks: 15

rittata/COPCs_transcriptomics

Transcriptome-based classification and risk prediction of chronic overlapping pain conditions.

Language: Jupyter Notebook - Size: 755 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 0 - Forks: 0

snaketron/scBubbletree

scBubbletree: quantitative tool for visual exploration of scRNA-seq data

Language: HTML - Size: 59.2 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 6 - Forks: 2

tucca-cellag/tucca-rna-seq

[UNDER-CONSTRUCTION] TUCCA's RNA-Seq Snakemake Workflow for Cellular Agriculture Projects

Language: Python - Size: 21.8 MB - Last synced at: about 5 hours ago - Pushed at: about 5 hours ago - Stars: 1 - Forks: 0

ngualand/ProOvErlap

ProOvErlap - Assessing feature proximity/overlap and testing statistical significance from genomic intervals

Language: Python - Size: 10.2 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

sales-lab/spatialDE

R wrapper for SpatialDE

Language: R - Size: 1.47 MB - Last synced at: 8 days ago - Pushed at: 27 days ago - Stars: 3 - Forks: 3

paulshuker/coppafisher Fork of reillytilbury/coppafish

COmbinatorial Padlock-Probe-Amplified Fluorescence In Situ Hybridization

Language: Python - Size: 242 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1 - Forks: 1

cantinilab/HuMMuS

Molecular interactions inference from single-cell multi-omics data

Language: R - Size: 79.4 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 24 - Forks: 4

rajewsky-lab/openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Language: HTML - Size: 175 MB - Last synced at: 17 days ago - Pushed at: 6 months ago - Stars: 97 - Forks: 17

iSEE/iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Language: R - Size: 17.9 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 225 - Forks: 43

kharchenkolab/pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

Language: JavaScript - Size: 78.4 MB - Last synced at: 20 days ago - Pushed at: about 1 year ago - Stars: 228 - Forks: 47

saezlab/cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Language: R - Size: 53.2 MB - Last synced at: 24 days ago - Pushed at: 2 months ago - Stars: 60 - Forks: 16

noncodo/BigRedButton

Pipeline for the unsupervised clustering of homologous RNA structure motifs from sequencing data.

Language: TeX - Size: 34.2 MB - Last synced at: 29 days ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 1

KatrionaGoldmann/volcano3D

An R package to plot interactive three-way differential expression analysis

Language: HTML - Size: 219 MB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 37 - Forks: 8

pinellolab/pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

Language: Python - Size: 23.6 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 47 - Forks: 5

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced at: 1 day ago - Pushed at: 2 months ago - Stars: 80 - Forks: 17

ELTEbioinformatics/mulea Fork of Biocodings/MulEA

mulea - an R package for enrichment analysis using various ontologies and empirical false discovery rate

Language: R - Size: 298 MB - Last synced at: 6 days ago - Pushed at: 5 months ago - Stars: 29 - Forks: 1

Related Keywords

transcriptomics 561 bioinformatics 163 rna-seq 115 genomics 88 r 72 single-cell 56 python 47 machine-learning 42 proteomics 38 gene-expression 32 visualization 32 scrna-seq 32 single-cell-rna-seq 28 differential-expression 25 omics 21 rnaseq 21 computational-biology 20 pipeline 20 metabolomics 19 rna-seq-analysis 19 spatial-transcriptomics 19 bioinformatics-pipeline 18 cancer 18 data-science 18 clustering 17 bioconductor 17 single-cell-analysis 14 nextflow 14 deep-learning 14 epigenomics 12 scanpy 12 rna-seq-pipeline 12 genetics 12 spatial 12 workflow 11 data-visualization 11 bioinformatics-analysis 11 database 10 transcriptome 10 shiny 10 differential-gene-expression 10 bash 10 systems-biology 10 rna 9 enrichment-analysis 9 snakemake 9 multi-omics 9 seurat 9 annotation 9 rstats 9 python3 8 reproducible-research 8 pathway-analysis 8 nanopore 8 alternative-splicing 8 bioinformatics-tool 8 data-analysis 8 ngs 7 visium 7 metagenomics 7 metabolism 7 statistics 7 assembly 7 meta-analysis 7 microbiome 7 drug-discovery 7 gene-set-enrichment 6 tcga 6 enrichment 6 docker 6 wrapper 6 omics-data-integration 6 imaging 6 pca 6 r-package 6 gene 6 rna-velocity 6 deconvolution 6 spatial-data 6 fastq 5 cdna 5 deseq2-analysis 5 salmon 5 microarray-data-analysis 5 rstudio 5 aging 5 drug-repurposing 5 snakemake-workflow 5 single-cell-genomics 5 network-analysis 5 random-forest 5 gsea 5 immunology 5 deseq2 5 genome 5 fastqc 5 illumina 5 scrna-seq-analysis 5 rnaseq-pipeline 5 genome-annotation 5

GitHub topics: transcriptomics

arc85/celltalker 📦

paulshuker/coppafisher Fork of reillytilbury/coppafish

ELTEbioinformatics/mulea Fork of Biocodings/MulEA

SyNUM-lab/NDD-Transcriptomics Fork of jarnokoetsier/NDD-Transcriptomics