scrna-seq-analysis

There are 130 repositories under scrna-seq-analysis topic.

  • hemberg-lab/scRNA.seq.course

    Analysis of single cell RNA-seq data course

    Language:TeX6736261360

  • zhanghao-njmu/SCP

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

    Language:R410813188

  • genecell/single-cell-papers-with-code

    Papers with code for single cell related papers

    27612070

  • dpeerlab/Palantir

    Single cell trajectory detection

    Language:Jupyter Notebook2301112652

  • wheaton5/souporcell

    Clustering scRNAseq by genotypes

    Language:Python1731123046

  • juexinwang/scGNN

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

    Language:Python13542840

  • KrishnaswamyLab/MELD

    Quantifying experimental perturbations at single cell resolution

    Language:Python1056269

  • 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.

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  • GfellerLab/SuperCell

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

    Language:R7051211

  • BaderLab/scClustViz

    Explore and share your scRNAseq clustering results

    Language:R4713489

  • dpeerlab/Harmony

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

    Language:Jupyter Notebook4682112

  • jyyulab/NetBID

    Data-driven Network-based Bayesian Inference of Drivers

    Language:R40799

  • quon-titative-biology/scAlign

    A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

    Language:R3451012

  • jaleesr/BITFAM

    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:R3111816

  • ejohnson643/EMBEDR

    Statistical quality evaluation of dimensionality reduction algorithms

    Language:Jupyter Notebook29592

  • paulranum11/SPLiT-Seq_demultiplexing

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

    Language:Python268108

  • fabilab/northstar

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

    Language:Python25236

  • IMB-Computational-Genomics-Lab/ascend

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

    Language:R226307

  • maclean-lab/RVAgene

    Recurrent Variational Auto gene encoder

    Language:Jupyter Notebook20335

  • JarningGau/ProjectSVR

    A package for reference mapping and nice visualization

    Language:R19240

  • JCVenterInstitute/FRmatch

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

    Language:R19762

  • mckellardw/scMuscle

    The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data

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  • xinhe-lab/GSFA

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

    Language:C++19362

  • JDBLab/Pancreas_ductal_scRNAseq

    The following repository contains code for all scRNAseq analysis and visualization performed in the paper: Single cell resolution analysis of the human pancreatic ductal progenitor cell niche

    Language:R17408

  • hamidghaedi/scRNA_seq-analysis

    scRNA analysis of public dataset on bladder cancer

    15214

  • infocusp/scaLR

    Single cell analysis using Low Resource

    Language:Python15350
  • Antler

    juliendelile/Antler

    R package for single-cell RNA-sequencing analysis

    Language:R15331

  • wtsi-hgi/yascp

    scRNA multimodal analysis pipeline utilised for large dataset processing

    Language:Python14427

  • jn-goe/gruffi

    Granular Functional Filtering (Gruffi) to isolate stressed cells

    Language:R121196

  • NMikolajewicz/scPipeline

    Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports

    Language:CSS11346

  • scmethods/scregclust

    Language:R92

  • tarot0410/BREMSC

    Novel joint clustering method with scRNA-seq and CITE-seq data

    Language:R8113

  • gdagstn/cellula

    Simple implementation of different single cell RNA-seq methods

    Language:R6221

  • 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:Python6211

  • snaketron/scBubbletree

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

    Language:HTML6332

  • VCCRI/scTalk

    Intercellular communication analysis for scRNA-seq data

    Language:R6761