GitHub topics: scrna-seq-data
ankitbioinfo/nico_tutorial
A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and covariation patterns between interacted cell types.
Language: Jupyter Notebook - Size: 62.5 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 3
seandavi/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Size: 1.43 MB - Last synced at: 11 days ago - Pushed at: about 2 months ago - Stars: 3,388 - Forks: 1,021
multitalk/miRTalk
Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data
Language: HTML - Size: 77 MB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 14 - Forks: 2
Harkany-Lab/Gueissaz_2025
This repository contains code to identify expression patterns of genes and cells involved in hypothalamic control of metabolism and stress response. It also performs bioinformatic molecular profile analysis of parvocellular and preautonomic neurons i.e. Crh. Overall, it enables reproducible analysis of biomarkers and ALK / Augα signaling in PVH
Language: BibTeX Style - Size: 119 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
GfellerLab/SuperCell
Coarse-graining of large single-cell RNA-seq data into metacells
Language: R - Size: 82.2 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 77 - Forks: 12
randel/MIND
Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution
Language: HTML - Size: 2.24 MB - Last synced at: 4 days ago - Pushed at: about 2 years ago - Stars: 45 - Forks: 9
nsalomonis/altanalyze
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
Language: Python - Size: 264 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 103 - Forks: 31
DaminK/GlobalGround-MetricLearning
This repository provides the python implementation of the AISTATS2025 paper "Global Ground Metric Learning with Applications to scRNA data" by Damin Kühn nad Michael T. Schaub.
Language: Jupyter Notebook - Size: 2.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
Perik-Zavodskii/ErythroOrigin
Predict human Erythroid cell tissue of origin using the BD Rhapsody single cell Immune responce panel gene expression data
Language: Jupyter Notebook - Size: 69.4 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
vandijklab/cell2sentence-ft
Cell2Sentence turns scRNA-seq data into text for LLM training.
Language: Python - Size: 229 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 81 - Forks: 13
Perik-Zavodskii/2ndDerivativeFeatures
Second Derivative-based selection of VariableFeatures
Language: Jupyter Notebook - Size: 19.3 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
umangv/picturedrocks
PicturedRocks Single Cell Analysis Tool
Language: Python - Size: 383 KB - Last synced at: 9 days ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0
Rongtingting/CNV_calling_Benchmark
Benchmarking records for scRNA-seq CNV detection.
Language: Python - Size: 2.03 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1
OlivierRaineteauSBRI/scRNASeq
Repo linked to our recent publication in Science Advances
Language: HTML - Size: 5.66 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
nlawlor/V-SVA
V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data
Language: R - Size: 22.8 MB - Last synced at: 12 months ago - Pushed at: over 5 years ago - Stars: 7 - Forks: 3
oscar-franzen/PanglaoDB
metadata and data from the database
Size: 50.6 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 28 - Forks: 8
mckellardw/scMuscle
The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data
Language: HTML - Size: 96.2 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 2
AllenInstitute/tasic2016data
Single cell transcriptomic data from Tasic, et al. (2016)
Language: R - Size: 100 MB - Last synced at: 1 day ago - Pushed at: over 6 years ago - Stars: 9 - Forks: 0
immunomind/covid19
🦠 Regularly updated list of publicly available datasets with single-cell (scRNAseq) and T-cell/antibody immune repertoire (AIRR / RepSeq / immunosequencing) data of COVID-19 patients with SARS-CoV-2.
Size: 470 KB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 41 - Forks: 4
himelmallick/BenchmarkSingleCell
Large-scale Benchmarking of Single-cell Differential Expression Analysis Methods
Language: R - Size: 16.9 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
Munfred/wormcells-data
Gene expression on C. elegans single cells
Language: HTML - Size: 165 KB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
inuritdino/HyperInflamDataProcessing
scRNA-seq datasets to support Jung et al, Sci Adv, 7(6): eabe5735, 2021. DOI: 10.1126/sciadv.abe5735
Language: R - Size: 168 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
UcarLab/V-SVA
V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data
Language: R - Size: 24 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
