GitHub topics: scrna-seq-analysis

Repositories

KrishnaswamyLab/MELD

Quantifying experimental perturbations at single cell resolution

Language: Python - Size: 17.9 MB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 109 - Forks: 9

dpeerlab/Palantir

Single cell trajectory detection

Language: Jupyter Notebook - Size: 56.2 MB - Last synced at: 5 days ago - Pushed at: 23 days ago - Stars: 252 - Forks: 54

wtsi-hgi/yascp

scRNA multimodal analysis pipeline utilised for large dataset processing

Language: Python - Size: 124 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 14 - Forks: 7

infocusp/scaLR

Single cell analysis using Low Resource

Language: Python - Size: 166 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 17 - Forks: 0

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: 12 days ago - Pushed at: 13 days ago - Stars: 6 - Forks: 3

viktormiok/scRNAseq_AdipocyteSubtyping

Python pipelines for analysis of adipocyte scRNA-seq data

Language: Jupyter Notebook - Size: 550 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 5 - Forks: 4

zhanghao-njmu/SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Language: R - Size: 788 MB - Last synced at: 16 days ago - Pushed at: about 1 year ago - Stars: 499 - Forks: 105

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

Language: R - Size: 61.6 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 31 - Forks: 17

GfellerLab/SuperCell

Coarse-graining of large single-cell RNA-seq data into metacells

Language: R - Size: 82.2 MB - Last synced at: 5 days ago - Pushed at: 10 months ago - Stars: 81 - Forks: 13

hds-sandbox/Intro-NGS-AU_course

Repository for the NGS summer course at Aarhus university

Language: Jupyter Notebook - Size: 173 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 8 - Forks: 4

kullrich/scTEI

scTEI - add any phylogenetically based transcriptome evolutionary index (TEI) to single-cell data objects

Language: HTML - Size: 61.1 MB - Last synced at: 7 days ago - Pushed at: 28 days ago - Stars: 2 - Forks: 0

asif7adil/scSPARKL

scSPARKL is an Apache spark based pipeline for performing variety of preprocessing and downstream analysis of scRNA-seq data.

Language: Python - Size: 94.7 KB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 5 - Forks: 1

TheHumphreysLab/CellScopes.jl Fork of HaojiaWu/CellScopes.jl

A Julia package for single cell and spatial data analysis

Language: Julia - Size: 96.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 1

YDaiLab/scRegulate

Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data

Language: Jupyter Notebook - Size: 3.16 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 0

dputhier/scigenex

This repository stores the scigenex R library.

Language: R - Size: 81.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 2

AntonioDeFalco/SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

Language: HTML - Size: 63 MB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 104 - Forks: 27

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

dpeerlab/Harmony

Harmony framework for connecting scRNA-seq data from discrete time points

Language: Jupyter Notebook - Size: 5.34 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 48 - Forks: 13

GuoBioinfoLab/STCAT

The single T cell annotation tool for scRNA-seq data

Language: Jupyter Notebook - Size: 22.5 MB - Last synced at: 20 days ago - Pushed at: about 2 months ago - Stars: 13 - Forks: 1

hemberg-lab/scRNA.seq.course Fork of rstudio/bookdown-demo

Analysis of single cell RNA-seq data course

Language: TeX - Size: 365 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 674 - Forks: 361

kleelab-bch/phet

PHet: Heterogeneity-Preserving Discriminative Feature Selection for Subtype Discovery

Language: Python - Size: 23.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 1

snaketron/scBubbletree

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

Language: HTML - Size: 59.2 MB - Last synced at: 30 days ago - Pushed at: 2 months ago - Stars: 6 - Forks: 2

Liuy12/STITCH

Spatial and single-cell Transcriptomics Integration Tool for CHaracterization (STITCH)

Language: R - Size: 3.35 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

scmethods/scregclust

Language: R - Size: 43.5 MB - Last synced at: 12 days ago - Pushed at: 5 months ago - Stars: 12 - Forks: 1

gdagstn/cellula

Simple implementation of different single cell RNA-seq methods

Language: R - Size: 85.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

torchstack-ai/cancer-biomarker-discovery

scRNASeq drug discovery and biomarker project

Language: R - Size: 154 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

JCVenterInstitute/FRmatch

Cell type matching in single-cell RNA-sequencing data using FR-Match

Language: R - Size: 156 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 19 - Forks: 3

AlicenJoyHenning/DamageToolReviewArticle

🗒️ Analysis scripts for the methods outlined in our review article evaluating scRNA-seq damaged cell detection strategies

Language: Jupyter Notebook - Size: 21.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

BaderLab/scClustViz

Explore and share your scRNAseq clustering results

Language: R - Size: 696 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 50 - Forks: 9

Svvord/FastCCC

A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies

Language: Jupyter Notebook - Size: 22.1 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1

jn-goe/gruffi

Granular Functional Filtering (Gruffi) to isolate stressed cells

Language: R - Size: 277 KB - Last synced at: 2 months ago - Pushed at: 7 months ago - Stars: 13 - Forks: 5

BehRoooz/scRNA-Seq-Pipeline

Nextflow-based pipeline for processing single-cell RNA sequencing (scRNA-Seq) data using Scanpy.

Language: Python - Size: 533 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

jawa23bio/cEpiReg

Our comprehensive database integrates data from scRNA seq and sc-ATAC seq, identifying cis-regulatory elements (CREs) through comparison with ENCODE, Epimap, GWAS Catalog, and other datasets. By connecting transcription factors (TFs), CREs, and target genes, cEpiReg unveils hidden regulatory links crucial for understanding AD pathogenesis.

Language: HTML - Size: 35.2 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

grnlab/airqtl

Single-cell eQTL mapping and causal gene regulatory network inference at high efficiency and accuracy

Language: Python - Size: 68.4 KB - Last synced at: 12 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 1

kris96tian/scRNA-WebApp

Interactive web application for analyzing scRNA-seq data using Scanpy

Language: Python - Size: 12.7 KB - Last synced at: 11 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

htejedam/SankeyPlot_CellChat

Generate Sankey plots from merged CellChat objects

Size: 0 Bytes - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

juexinwang/scGNN

scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

Language: Python - Size: 68.4 MB - Last synced at: 5 months ago - Pushed at: 11 months ago - Stars: 140 - Forks: 40

liyarubio/VeloGIF

The integration tool for 15 single cell RNA velocity algorithms

Language: Python - Size: 20 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

j-rub/scVital

Deep Learning Algorithm for cross-species integration of scRNA-seq data

Language: Jupyter Notebook - Size: 2.29 MB - Last synced at: 12 days ago - Pushed at: 6 months ago - Stars: 3 - Forks: 0

LabOnoM/GSE284271

Single Cell Spatial Transcriptomics of the Murine Embryonic Palate Links Pax9 to Patterning and Organization of Extracellular Matrix Components

Language: Jupyter Notebook - Size: 786 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

jyyulab/NetBID

Data-driven Network-based Bayesian Inference of Drivers

Language: R - Size: 360 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 40 - Forks: 9

Matrisome/MatriCom

MatriCom: matrisome communications in single-cell RNA-seq datasets

Language: R - Size: 5.92 MB - Last synced at: 6 months ago - Pushed at: 6 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

wheaton5/souporcell

Clustering scRNAseq by genotypes

Language: Python - Size: 1.66 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 168 - Forks: 46

IMB-Computational-Genomics-Lab/ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)

Language: R - Size: 256 MB - Last synced at: 2 months ago - Pushed at: almost 6 years ago - Stars: 22 - Forks: 7

guachinwey/Analysis-of-scRNA-seq-samples-for-prostate-tumour-tissue-at-different-stages-of-the-cell-cycle

Language: R - Size: 43.9 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

mckellardw/DWM_utils

Tools, wrappers, utilities, and resources for handling single-cell and spatial transcriptomics data

Language: Python - Size: 60.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 3

iliapopov17/BI-Workshop-miniProjects

📚Workshop study projects in Bioinformatics Institute 2023-2024

Language: Jupyter Notebook - Size: 18.3 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

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

bramadi/scBenchmarker

Size: 1000 Bytes - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

argo-bio/iMOS-LTBR-as-myeloid-checkpoint

These are scripts for LTBR as a novel myeloid checkpoint for cancer immunotherapy

Language: R - Size: 829 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

inesmarais/scRNA-seq-analysis-cornea

Scripts for analysis of transcriptomic data of the developing cornea

Language: Jupyter Notebook - Size: 21.7 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

elolab/Hitchhikers_Guide_scRNAseq_course

The Hitchhiker's Guide to scRNA-seq

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Beth526/scRNAseq_alt_transcripts

Finding and analyzing alternate poly-A sites in 3' scRNA-seq 10X files

Language: Python - Size: 2.44 MB - Last synced at: 11 months ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

XingyanLiu/stagewiseNN

Constructing a developmental tree from scRNA-seq data

Language: Python - Size: 148 MB - Last synced at: 26 days ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1

luglilab/SP025_Analysis

Integration analysis with Scanpy and scRNAseq TME from blueprint

Language: Jupyter Notebook - Size: 256 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

elolab/Bioinfo_Tcell_projects_22

EMBL-EBI scRNA Bioinformatics T cell course 2022

Language: HTML - Size: 91.7 MB - Last synced at: 10 months ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1

JCVenterInstitute/celligrate

Software suite for marker gene identification and cell type integration from single cell RNA-sequencing data

Language: HTML - Size: 24.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

mpaltsai/scRNA-Explorer

scRNA-Explorer pipeline allows users to interrogate in an interactive manner scRNA-sequencing data sets to explore via gene expression correlations possible function(s) of a gene of interest

Language: R - Size: 51 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

SuhasSrinivasan/multiplexed-scrna

Multiplexed droplet scRNA-seq Kang et al Nat Biotechnol 2018

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kAI-swa/M2ASDA

Manipulate scRNA-seq data with GSASD

Language: Python - Size: 1.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

volpesofi/iGCA_scRNAseq_analysis

Analysis scripts for "Aging, inflammation and DNA damage in the somatic testicular niche with idiopathic germ cell aplasia" publication

Language: Jupyter Notebook - Size: 10.2 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

fabilab/northstar

Single cell type annotation guided by cell atlases, with freedom to be queer

Language: Python - Size: 304 KB - Last synced at: 9 days ago - Pushed at: almost 3 years ago - Stars: 25 - Forks: 6

JarningGau/ProjectSVR

A package for reference mapping and nice visualization

Language: R - Size: 105 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 12 - Forks: 0

ForwardStar/sctreeshap

An effective tool for single-cell RNA sequencing.

Language: Python - Size: 418 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

bixBeta/scRNA-WS24

Exercises for scRNA-seq Workshop TREX x BioHPC 2024.

Language: Jupyter Notebook - Size: 11.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 2

garifalloj/Scott-Gordon-Laboratory-CHOP-scRNAseq_Uterine_Macrophages_NK_Project

Repository to store and share all related code for the Uterine macrophages and NK cells Project from the Scott Gordon Laboratory at the Children's Hospital of Philadelphia

Language: R - Size: 48.8 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

VCCRI/scTalk

Intercellular communication analysis for scRNA-seq data

Language: R - Size: 5.36 MB - Last synced at: 2 months ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 1

Farber-Lab/assignClustID

R package to assign ID to genotypes created by Souporcell

Language: R - Size: 1.19 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

OlivierRaineteauSBRI/scRNASeq

Repo linked to our recent publication in Science Advances

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ToureLaminelab/RNAvelocity

RNA velocity is a high-dimensional vector that predicts the future state of individual cells on a timescale of hours.

Language: Jupyter Notebook - Size: 43.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

HallDaveNineteenNintysix/tocelldb

Customize your specific organism cellchatdb

Language: R - Size: 118 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

thuylinhmk/scRNA-seq-analysis

Basic pipeline of scRNA-seq downstream analysis

Language: Jupyter Notebook - Size: 132 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

thekaplanlab/CilioGenics_Analysis

CilioGenics is an integrated method for predicting the ciliary genes

Language: R - Size: 94 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

Moha-cm/single_cell_Trajectory

Dashboard for ScRNAseq Trajectory Analysis

Language: HTML - Size: 3.61 MB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

raveancic/scRNAaltas_TNBC_mm

Language: Python - Size: 22.5 KB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 2

stevehxf/GINS_NCB2023

single cell RNA-seq analysis of human gastric insulin-secreting (GINS) organoids

Language: R - Size: 150 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

mcrewcow/BaranovLab

Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

Language: Jupyter Notebook - Size: 64.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

kullrich/orthomap 📦

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

Language: Python - Size: 59.1 MB - Last synced at: 22 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 1

genecell/single-cell-papers-with-code

Papers with code for single cell related papers

Size: 44.9 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 225 - Forks: 47

peterwolf4/MRCO

Multi Resolution Cluster Optimization

Language: R - Size: 3.75 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

HCBravoLab/iDA

iDA: dimensionality reduction for latent structure discovery

Language: R - Size: 208 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 4

quon-titative-biology/scBFA

Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data

Language: R - Size: 4.4 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 2

paulranum11/SPLiT-Seq_demultiplexing

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Language: Python - Size: 6.83 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 25 - Forks: 9

xinhe-lab/GSFA

R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single-cell CRISPR screening data.

Language: C++ - Size: 1.32 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 1

dgavr/Single_Cell_Iterative_Pooling

Iteratively randomly pooling scRNA-seq expressing a given gene from different numbers of cells and running DESeq2 with fdrtools correction to determine how many times which genes come out as enriched with said gene

Language: Python - Size: 16.6 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

stefanie-baerthel/combinatorial_treatment_analysis

KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted therapies, immune checkpoint blockade and engineered T cells. In this study, we performed a systematic high throughput combinatorial drug screen and identified a synergistic interaction between the MEK inhibitor trametinib and the multi- kinase inhibitor nintedanib. Using single cell RNA sequencing and immunophenotyping, we show that the combination therapy reprograms the immunosuppressive microenvironment and primes cytotoxic and memory T cells to infiltrate the tumors, thereby sensitizing mesenchymal PDAC to PD-L1 inhibition.

Language: Jupyter Notebook - Size: 70.7 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

nickwawee/MSU_Ad_Hoc_Analyses

This repo contains code and presentations used for ad-hoc analyses regarding liver cell toxicology and development. It also contains analyses on human and mice immune cells.

Size: 29.5 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

JulianSpagnuolo/adtseq

adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data

Language: C++ - Size: 69.3 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

PrincyJohnson/Single-cell-RNA-sequencing

Objectives are to:  Optimise the scRNA-seq data approach using Seurat by investigating the effects of QC and background correction for healthy and a diabetic dataset of the mouse retina.  Perform differential gene expression.  Perform clustering of the different retinal cell types from the scRNA-Seq data by assessing a range of publicly available algorithms.  Identify the cell-types for both control and diabetic retinal dataset.  Try to install different deconvolution packages that suits the project.  Use them to identify cell-type proportions from bulk data guided by the scRNAseq data  Compare the results to identify the best proportions and the most affected cell-types.

Language: R - Size: 30.3 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0