GitHub topics: transcriptomics

Repositories

cran-task-views/Omics

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

Size: 81.1 KB - Last synced at: about 20 hours ago - Pushed at: about 22 hours ago - Stars: 21 - Forks: 5

owkin/PyDESeq2

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

Language: Python - Size: 1.38 MB - Last synced at: about 19 hours ago - Pushed at: 4 days ago - Stars: 675 - Forks: 78

dvoelkl/HIDE

Implementation of HIDE as proposed in Völkl et al (2025), HIDE: Hierarchical cell-type Deconvolution

Language: Python - Size: 83.1 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 3 - Forks: 0

JRaviLab/compbio-gists

Computational Biology & Bioinformatics Resources

Language: Shell - Size: 39.1 KB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 15 - Forks: 4

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)

Language: R - Size: 71.3 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

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: 6.66 MB - Last synced at: about 24 hours ago - Pushed at: 2 days ago - Stars: 12 - Forks: 5

obophenotype/cell-ontology

An ontology of cell types

Language: Makefile - Size: 563 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 181 - Forks: 53

Chaibioinfo/Transcriptomics

Transcriptome Profiling of Stress Responses in Cyamopsis tetragonoloba Using RNA-Seq and Differential Gene Expression Analysis

Size: 4.88 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

number-25/rich_directRNA

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

Language: Nextflow - Size: 7.79 MB - Last synced at: 1 day ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

PavlidisLab/gemma.R

An R wrapper for the Gemma RESTful API

Language: R - Size: 85.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 10 - 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: 11.6 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 8 - Forks: 0

scverse/anndata

Annotated data.

Language: Python - Size: 5.9 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 651 - Forks: 171

Sri953/scRNAseq_Human_OSNs

Research Project on Discovering Triggers of Action Potentials in Human Olfactory Sensory Neurons

Size: 4.38 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

scverse/scanpy

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

Language: Python - Size: 41.1 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2,174 - Forks: 659

ablab/IsoQuant

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

Language: Python - Size: 20 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 177 - Forks: 19

markziemann/dee2

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

Language: Shell - Size: 56.2 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 42 - Forks: 7

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.64 GB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 264 - Forks: 331

mohansree14/Prediction-of-Cellular-Mechanisms-Alzheimer--Disease

Analyze single-cell RNA and spatial transcriptomics data to uncover cellular mechanisms in Alzheimer’s Disease. Includes data cleaning, feature engineering, visualization, and machine learning modeling.

Language: Jupyter Notebook - Size: 20.2 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

tidyomics/tidySummarizedExperiment

Brings SummarizedExperiment to the tidyverse

Language: R - Size: 6.04 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 26 - Forks: 7

stemangiola/tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

Language: R - Size: 107 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 174 - Forks: 25

bnjenner/impaqt

Identifies Multiple Peaks and Qauntifies Transcripts. Quantifies gene expression from TAGseq experiments by identifying transcript isoforms containing distinct 3' UTRs/terminal exons.

Language: C++ - Size: 70.9 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 0

LieberInstitute/spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

Language: HTML - Size: 14.9 GB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 22 - Forks: 4

keller-mark/awesome-biological-visualizations

A list of web-based interactive biological data visualizations.

Size: 141 KB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 206 - Forks: 19

AllenInstitute/scrattch

Single cell RNA-seq analysis for transcriptomic type characterization

Language: HTML - Size: 97.9 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 37 - Forks: 3

PejLab/Pantry

Pan-transcriptomic phenotyping

Language: Python - Size: 14.6 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 18 - Forks: 0

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 88 - Forks: 18

chanzuckerberg/cellxgene

An interactive explorer for single-cell transcriptomics data

Language: JavaScript - Size: 239 MB - Last synced at: 5 days ago - Pushed at: 20 days ago - Stars: 710 - Forks: 140

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 156 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 44 - Forks: 9

pachterlab/gget

🧬 gget enables efficient querying of genomic reference databases

Language: Python - Size: 330 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 1,049 - Forks: 77

ellfran-7/cluefish

A specialised workflow designed to enhance the biological interpretation of transcriptomic data series 🎣

Language: R - Size: 31.7 MB - Last synced at: 1 day ago - Pushed at: 10 days ago - Stars: 3 - Forks: 1

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: 7.08 MB - Last synced at: about 23 hours ago - Pushed at: 1 day ago - Stars: 65 - Forks: 25

GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

Language: Python - Size: 5 MB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 156 - Forks: 23

Martinaa1408/AG_project

This project focuses on the hybrid genome and transcriptome analysis of compost-derived fungal isolates with bioplastic-degrading potential. It delivers high-quality Nanopore + Illumina assemblies, functional annotation, and RNA-Seq profiling to identify PLA/PHA-degrading enzymes supporting environmental biotechnology.

Size: 49.2 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

wangdian-PKU/CrossTx

Cross-Species Tumor Transcriptomic Similarity Analysis R package

Language: R - Size: 16.1 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 0

scverse/decoupler

Python package to perform enrichment analysis from omics data.

Language: Python - Size: 112 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 219 - Forks: 35

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: 3.95 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 191 - Forks: 16

Melclic/intersectomics

Package to study time series (or other series) multi-omics patterns of expresssion with replicates

Language: Python - Size: 1.52 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0

owkin/fedpydeseq2

A federated implementation of PyDESeq2, based on Substra.

Language: Python - Size: 2.45 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 13 - Forks: 0

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: 34.8 MB - Last synced at: 10 days ago - Pushed at: 2 months ago - Stars: 533 - Forks: 195

GoekeLab/sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Language: R - Size: 2.16 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 132 - Forks: 27

AhmedSAHassan/DoReMiTra

Orchestrating Blood Radiation Transcriptomic Data

Language: R - Size: 435 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

AllenInstitute/scrattch.vis

scRNA-seq data visualization from scrattch

Language: R - Size: 104 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 27 - Forks: 2

AllenInstitute/scrattch.hicat

Hierarchical, iterative clustering for analysis of transcriptomics data in R

Language: HTML - Size: 155 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 114 - Forks: 31

Saddeekhan/Flowering-time-genes-

This project provides a Python-based workflow for analyzing and visualizing flowering time gene expression from RNA-seq data. It includes preprocessing steps such as missing value imputation and normalization, followed by clustering and statistical summaries of expression patterns across developmental stages (M1–M8).

Language: Jupyter Notebook - Size: 496 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 0 - Forks: 0

Marval96/Transcriptomics_UIVC

Transcriptomics analysis (RNAseq bulk) of macrophages in the breast cancer tumour microenvironment (BrCa).

Language: Jupyter Notebook - Size: 15.8 MB - Last synced at: 18 days ago - Pushed at: 19 days ago - Stars: 3 - Forks: 2

DiseaseTranscriptomicsLab/markeR

🧬 Toolkit for Evaluating Gene Sets as Phenotype Markers in R

Language: R - Size: 152 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 4 - Forks: 0

spacetx/starfish

starfish: unified pipelines for image-based transcriptomics

Language: Python - Size: 114 MB - Last synced at: 2 days ago - Pushed at: 25 days ago - Stars: 237 - Forks: 70

ZJUFanLab/scCATCH

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

Language: R - Size: 52 MB - Last synced at: 6 days ago - Pushed at: over 2 years ago - Stars: 231 - Forks: 36

GuyTeichman/RNAlysis

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

Language: Python - Size: 797 MB - Last synced at: about 3 hours ago - Pushed at: 3 months ago - Stars: 138 - Forks: 13

Ifthekarhussain/Single-cell-RNA-seq-analysis-of-lung-cancer-NSCLC-

Single-cell RNA-seq analysis of lung cancer (NSCLC) using Seurat, SingleR, and Monocle3. Includes QC, clustering, marker identification, pathway enrichment, and pseudotime analysis.

Language: R - Size: 1.17 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 0 - Forks: 0

definecoder/PLAGL1-server

A user-friendly GUI for transcriptomic data analysis and biomarker discovery.

Language: Python - Size: 135 MB - Last synced at: 13 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

giannarelli-lab/Systems-immunology-based-drug-repurposing-framework-to-target-inflammation-in-atherosclerosis

Code used for data analysis of drug repurposing approach to target inflammation in atherosclerosis

Language: HTML - Size: 6.34 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 3 - Forks: 1

theislab/DRVI

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Language: Python - Size: 14 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 48 - Forks: 3

czbiohub-sf/tabula-sapiens

Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens

Language: Jupyter Notebook - Size: 790 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 42 - Forks: 9

PavlidisLab/rnaseq-pipeline

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

Language: Shell - Size: 43.6 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 24 - Forks: 5

plasslab/SCALPEL

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

Language: R - Size: 646 KB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 22 - Forks: 1

BiomedSciAI/biomed-multi-omic

Build foundation model on RNA or DNA data

Language: Jupyter Notebook - Size: 32.8 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 24 - Forks: 6

CogDisResLab/drugfindR

Repository holding the code for the drugfindR R package

Language: R - Size: 7.13 MB - Last synced at: 1 day ago - Pushed at: 24 days ago - Stars: 8 - Forks: 3

eidanmoore/Bulk-RNA-seq-analysis-on-Gout-data

A short bulk RNA-seq analysis performed in R based on a class-provided gout dataset. Code is adapted and expanded to facilitate a basic RNA-seq workflow starting from DEseq2 data, including analysis such as volcano plots, PCA, immune cell deconvolution and heatmap creation.

Size: 5.2 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0

lasseignelab/230926_EJ_Setbp1_AlternativeSplicing

This repository is for our 2024 manuscript, Cell-type-specific alternative splicing in the cerebral cortex of a Schinzel-Giedion Syndrome patient variant mouse model

Language: R - Size: 128 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 1 - Forks: 0

CohenLabUGA/SAB_isolates

Language: Jupyter Notebook - Size: 233 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

tucca-cellag/tucca-rna-seq

Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects

Language: Python - Size: 31.3 MB - Last synced at: 2 days ago - Pushed at: 8 days ago - Stars: 7 - Forks: 0

epigen/macrophage-regulation

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

Language: Jupyter Notebook - Size: 29.1 MB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 1

paulshuker/coppafisher Fork of reillytilbury/coppafish

COmbinatorial Padlock-Probe-Amplified Fluorescence In Situ Hybridization

Language: Python - Size: 242 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 1

theislab/mapqc

MapQC - a metric for the evaluation of single-cell query-to-reference mappings

Language: Python - Size: 31.8 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 9 - Forks: 1

SML-CompBio/OncoMark

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

Language: Jupyter Notebook - Size: 21.9 MB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 3 - Forks: 0

ddiez/singleCellHaystack-py

Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).

Language: Python - Size: 69 MB - Last synced at: 14 days ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 1

GoekeLab/bambu

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

Language: R - Size: 550 MB - Last synced at: 17 days ago - Pushed at: 18 days ago - Stars: 215 - Forks: 24

rajewsky-lab/openst

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

Language: HTML - Size: 178 MB - Last synced at: 21 days ago - Pushed at: 2 months ago - Stars: 104 - Forks: 18

SimonHegele/rnaQAUSTcompare

Small python CLT that generates a comparative plot for multiple rnaQUAST reports

Language: Python - Size: 4.31 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

layanomics/CrispAstro-Seq

End-to-end, reproducible RNA-seq pipeline replicating a published CRISPR-knockout study in human astrocytes (GSE185726), using STAR, DESeq2 (R), and cloud-based Bash workflows.

Language: Jupyter Notebook - Size: 26.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

alperoglu/ASTRID

Tool for quick and standardized annotation of single cell transcriptomics data

Language: Jupyter Notebook - Size: 163 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

ShakiraSA/Personal-Project-Using-perl-and-R-for-the-automatization-of-a-microarray-pipeline

Integration of Perl script into data processing pipeline

Language: HTML - Size: 771 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

bhardwaj-lab/scChICflow

Workflow for processing single-cell ChIC (Chromatin ImmunoCleavage) data

Language: Python - Size: 27.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

gabrielramirezv/leukemia_gene_expression

Leukemia is a cancer of blood-forming tissues. For this reason, it is relevant to analyze the differences in gene expression for people affected by this disease, which is the purpose of this project.

Language: Shell - Size: 1.98 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

Alexis-Varin/RightOmicsTools

An R package providing tools for single-cell RNA-seq data analysis

Language: R - Size: 9.82 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 0

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: 20 days ago - Stars: 234 - Forks: 47

nf-core/molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

Language: Nextflow - Size: 6.57 MB - Last synced at: 1 day ago - Pushed at: 2 months ago - Stars: 13 - Forks: 12

Augroup/miniQuant

Improving gene isoform quantification with miniQuant

Size: 72.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 24 - Forks: 2

elisabettasciacca/multiDEGGs

An R package to perform differential network analysis in single and multi-omic data. It can also be used for feature selection in ML.

Language: R - Size: 10.7 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

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: 12 days ago - Pushed at: over 1 year ago - Stars: 65 - Forks: 36

aljpetri/isONclust3

De novo clustering of long transcript reads into genes

Language: Rust - Size: 9.76 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 16 - Forks: 3

bioinfonupeb/transcriptomic_analysis_lep

Transcriptomic analysis.

Language: Shell - Size: 43.9 KB - Last synced at: about 1 month ago - Pushed at: about 1 month 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: about 1 month ago - Pushed at: about 1 month ago - Stars: 51 - Forks: 9

Osama1452/RNA-Seq-experiment

A state-of-the-art R pipeline for RNA-seq data analysis, optimized for differential expression and functional annotation in mouse models. Features edgeR-based modeling, limma contrasts, and clusterProfiler for GO/KEGG insights. A valuable resource for genomic research and publication.

Language: HTML - Size: 94.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0