single-cell-atac-seq

There are 2 repositories under single-cell-atac-seq topic.

• zhanghao-njmu / SCP

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

  single-cellseurat-objectssingle-cell-analysissingle-cell-rna-seqscrna-pipelinescrna-seqscrna-seq-analysisseuratscanpyanndatasingle-cell-omicssingle-cell-sequencingshiny-appsshiny-appshinyappssingle-cell-atac-seqsingle-cell-genomicssingle-cell-pipelinescatac-seq
  Language:R 296

• r3fang / SnapATAC

  Analysis Pipeline for Single Cell ATAC-seq

  single-cell-atac-seqsingle-cell-analysisbioinformatics-pipelineepigeneticsmachine-learning-algorithmssequencing
  Language:R 295

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

  Papers with code for single cell related papers

  single-cellscrna-seqscrna-seq-analysisreproducible-researchreproducible-sciencesingle-cell-omicssingle-cell-atac-seqpaper-with-code
  254

• yanwu2014 / swne

  Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

  single-cell-rna-seqsingle-cell-analysisdata-visualizationdimensionality-reductionnonnegative-matrix-factorizationbioinformaticssingle-cell-genomicsstatistical-methodssingle-cell-atac-seq
  Language:R 102

• parashardhapola / scarf

  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

  bioinformaticssingle-cell-genomicssingle-cell-rna-seqdimension-reductionclusteringumaptsnebig-datacite-seqsingle-cell-atac-seqmemory-efficientscalable-data-analysisscrna-seqscatac-seqpseudotimemultiomicsgene-modulesdifferential-expressiongraph-analyticsgenomics
  Language:Python 88

• genecell / COSG

  Accurate and fast cell marker gene identification with COSG

  single-cellsingle-cell-rna-seqsingle-cell-analysissingle-cell-atac-seqspatial-transcriptomics
  Language:Jupyter Notebook 35

• Taiji-pipeline / Taiji

  All-in-one analysis pipeline

  atac-seq-pipelinerna-seq-pipelinesingle-cell-atac-seqsingle-cell-rna-seqtranscriptional-regulatory-network
  Language:Haskell 33

• quadbio / scMultiome_analysis_vignette

  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis

  bioinformaticssingle-cell-analysissingle-cell-multiomicstutorialsingle-cell-atac-seqsingle-cell-rna-seq
  29

• r3fang / snATAC

  <<------ Use SnapATAC!!

  single-cell-atac-seqsingle-cell-analysissingle-cell-genomicsbioinformatics-pipelineclustering
  Language:Python 25

• p4rkerw / Muto_Wilson_NComm_2020

  Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

  allele-specific-expressionbioinformaticsgenomicskidneysingle-cellsingle-cell-atac-seqsingle-cell-rna-seq
  Language:R 22

• SUwonglab / scABC

  atac-seqsingle-cellsingle-cell-atac-seq
  Language:HTML 18

• p4rkerw / Wilson_Muto_NComm_2022

  Containerized workflow for analysis of human diabetic kidney disease by snRNA-seq and snATAC-seq

  allele-specificckddiabetesheritabilitykidneysingle-cell-atac-seqsingle-cell-rna-seqsingle-cell-sequencing
  Language:R 11

• cellgeni / cellatac

  Sanger Cellular Genetics single-cell ATAC-seq pipeline.

  atac-seqatac-seq-pipeline10x-genomicsnextflow-pipelinesingle-cell-atac-seq
  Language:Nextflow 10

• kpatel427 / multiome_analysis

  Scripts for sincle cell multiome analysis

  seuratsingle-cell10xgenomicsseurat-objectssingle-cell-rna-seqsingle-cell-analysissingle-cell-atac-seq
  Language:R 9

• JGASmits / AnanseSeurat

  Single cell ANANSE Gene-regulatory-network analysis from Seurat objects

  single-cellsingle-cell-atac-seqsingle-cell-rna-seqgrn-analysisrseurat-objects
  Language:R 8

• p4rkerw / SALSA

  Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts

  allele-specificbioinformaticsgenotypesingle-cellsingle-cell-atac-seqsingle-cell-rna-seq
  Language:Shell 4

• xindong95 / SCRIP

  SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-cell resolution based on scATAC-seq.

  single-cellsingle-cell-atac-seq
  Language:C 3

• quon-titative-biology / scBFA

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

  human-cell-atlassingle-cellscrna-seqscrna-seq-analysissingle-cell-genomicssingle-cell-atac-seq
  Language:R 2

• OpenOmics / cell-seek

  One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.

  single-cell-atac-seqsingle-cell-omicssingle-cell-rna-seq10xgenomicssingle-cell-vdjsingle-cell-cite-seq
  Language:Python 1

• yuelaiwang / CEMBA_AMULET_Scrublet

  Comparison of the performance of AMULET and modified Scrublet on doublet removal in the CEMBA2.0 project.

  ngssingle-cell-atac-seq
  Language:Python 1

• Hattyoriiiiiii / single-cell-scripts

  scripts for scRNA-Seq/scATAC-Seq

  atac-seqbioinformaticsepigeneticsngsngs-analysisrna-seqscatacseqscrnaseqsingle-cellsingle-cell-analysissingle-cell-atac-seqsingle-cell-rna-seq
  Language:R 0

• p4rkerw / Wilson_GBio_2024

  Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease

  aneuploidyckdcopy-number-variationkidneysingle-cellsingle-cell-atac-seqsingle-cell-genomicssingle-cell-multiomicssingle-cell-rna-seqspatial-transcriptomicsloss-of-y-chromosomemosaic-chromosomal-alterationssomatic-mosaicism
  Language:R 0

• poloarol / single-cell-transcriptomics-app

  A R Shiny App for single-cell analysis

  rshinyrshiny-applicationsingle-cell-analysissingle-cell-atac-seqsingle-cell-genomicssingle-cell-omicssingle-cell-rna-seq
  Language:R 0

• aryarm / sc_rats

  Analyzing single cell ATAC data from the brains of drugged rats

  single-cell-atac-seqneurosciencerattus-norvegicus
  Language:Jupyter Notebook

• tAndreani / scATAC-benchmarking

  Benchmarking computational single cell ATAC-seq methods

  benchmarkmachine-learningsingle-cell-atac-seq
  Language:Jupyter Notebook

• ytanaka-bio / cisMultiDeep

  Workflow to identify functional cis-regulatory regions for each annotated cell type

  cis-regulatory-elementscross-speciesdeep-learningenhancershi-cpromotersshapsingle-cell-atac-seqsingle-cell-methylationsingle-cell-multiomicssingle-cell-rna-seq
  Language:Python