scatac-seq

There are 4 repositories under scatac-seq topic.

zhanghao-njmu / SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
single-cell seurat-objects single-cell-analysis single-cell-rna-seq scrna-pipeline scrna-seq scrna-seq-analysis seurat scanpy anndata single-cell-omics single-cell-sequencing shiny-apps shiny-app shinyapps single-cell-atac-seq single-cell-genomics single-cell-pipeline scatac-seq
Language:R 559
liulab-dfci / MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
scatac-seq scrna-seq epigenetics snakemake-workflows transcription-factors gene-regulatory-networks
Language:C 291
scverse / muon
muon is a multimodal omics Python framework
multimodal-data multimodal-omics-analysis multi-omics anndata scanpy mudata muon scrna-seq scatac-seq cite-seq scverse
Language:Python 247
pinellolab / STREAM
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
singlecell trajectory lineage visualization scatac-seq scrna-seq python
Language:Jupyter Notebook 176
sanderlab / scPerturb
scPerturb: A resource and a python/R tool for single-cell perturbation data
cite-seq database perturbation python r scatac-seq science scrna-seq single-cell statistics
Language:Jupyter Notebook 146
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.
bioinformatics single-cell-genomics single-cell-rna-seq dimension-reduction clustering umap tsne big-data cite-seq single-cell-atac-seq memory-efficient scalable-data-analysis scrna-seq scatac-seq pseudotime multiomics gene-modules differential-expression graph-analytics genomics
Language:Python 102
sankaranlab / SCAVENGE
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
cell-heterogeneity cell-state cell-trajectory complex-traits disease-mechanisms fine-mapping network-propagation random-walk scatac-seq single-cell-analysis causal-celltype gwas-tool single-cell disease-celltype
Language:R 88
alexisvdb / singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
bioinformatics single-cell r transcriptomics spatial-transcriptomics cite-seq pseudotime scatac-seq spatial-proteomics
Language:R 85
genecell / COSGR
Accurate and fast cell marker gene identification with COSG
scrna-seq scatac-seq spatial-transcriptomics marker-genes
Language:R 62
aertslab / CREsted
CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
deep-learning regulatory-genomics single-cell-genomics scverse scatac-seq sequence-models
Language:Python 47
shiquan / PISA
A collection of tools to process single-cell omics datasets.
single-cell scrna-seq scatac-seq
Language:C 44
wukevin / babel
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
single-cell scrna-seq scatac-seq deep-neural-networks multi-omics
Language:Jupyter Notebook 43
CellScopes.jl
HaojiaWu / CellScopes.jl
A Julia package for single cell and spatial data analysis
bioinformatics cartana data-viz julia-package merfish scatac-seq scrna-seq seqfish single-cell-omics slideseq spatial-transcriptomics starmap visium xenium
Language:Julia 41
swaruplabUCI / ArchRtoSignac
An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
r scatac-seq
Language:R 35
aertslab / single_cell_toolkit
Tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.
hydrop scatac-seq
Language:Shell 27
pinellolab / pychromVAR
A python package for chromVAR
chromatin-accessibiity chromvar scatac-seq
Language:Python 27
jumphone / BEER
BEER: Batch EffEct Remover for single-cell data
single-cell-analysis batch-effects scrna-seq scatac-seq umap
Language:R 24
caleblareau / mtscATACpaper_reproducibility
Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
lineage mitochondria r scatac-seq
Language:HTML 16
biobenkj / compartmap
Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
scrna-seq scatac-seq
Language:R 14
mvinyard / ArchR-h5ad
Parse ArchR arrow files to anndata h5ad
io r-to-python scatac-seq single-cell
Language:Python 13
AllenInstitute / aifi-swanson-teaseq
Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization
tea-seq icicle-seq atac-seq scatac-seq
Language:R 11
csbg / neuroblastoma
Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis
bone-marrow heterogeneity metastasis microenvironment monocytes neuroblastoma scatac-seq scrna-seq single-cell
Language:Jupyter Notebook 9
SUwonglab / sc-compReg
R package for single-cell comparative regulatory analysis
comparative-regulatory-analysis scatac-seq scrna-seq
Language:R 7
aertslab / scatac_fragment_tools
Tools for working with scATAC-seq fragment files
fragment fragments scatac-seq single-cell
Language:Python 6
AprilYuge / ATAC-annotation-benchmark
scripts for manuscript 'benchmarking automated cell type annotation tools for single-cell ATAC-seq data'
scrna-seq benchmark classification scatac-seq
Language:Jupyter Notebook 6
bowang-lab / simATAC
A single-cell ATAC-seq simulation framework (R package)
scatac-seq simulator software
Language:R 6
raevskymichail / epi-impute
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
epigenetics imputation integration multiomics scatac-seq scrna single-cell chromatin
Language:R 5
shuzwang / P2_cochlea
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
single-cell-omics gene-regulatory-network multiomics cochlea scrna-seq scatac-seq
Language:R 5
Barski-lab / sc-seq-analysis
CWL toolkit for single-cell sequencing data analysis
bioinformatics genomics rna-seq single-cell 10x 10x-genomics cwl fair scatac-seq scrna-seq workflow
Language:Common Workflow Language 4
gtca / chame
Chromatin analysis module
atac-seq chromatin genome multiome ranges scatac-seq scverse
Language:Python 4
jumphone / InferLoop
InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop
chromatin-structure scatac-seq single-cell-3d-genome-structure single-cell-chromatin-accessibility single-cell-multi-omics spatial-chromatin-accessibility
Language:R 4
scASAP
cfusterot / scASAP
single-cell ATAC Sequencing Analysis Pipeline
pipeline scatac-seq
Language:HTML 2
hyunsoo77 / maleBC_single_cells
This repository is for male breast cancer scRNA-seq and scATAC-seq data processing and figure generation.
breast-cancer male-breast-cancer rna-seq scatac-seq scrna-seq single-cell
Language:Jupyter Notebook 2
lab-conrad / resVAE-ensemble
resVAE-ensemble: feature identification in single-cell data
deep-ensemble scatac-seq scrna-seq single-cell-analysis
Language:Jupyter Notebook 2
csbg / fibroblast-perturb-seq-analysis
Epigenetic regulators of fibrotic transformation in cardiac fibroblasts
cardiac-fibrosis fibroblasts perturb-seq scatac-seq scrna-seq
Language:Jupyter Notebook 1
manishabarse / scATAC-seq-and-scRNA-seq-Integration-Analysis-in-Adult-Mouse-Brain
r-markdown r-studio scatac-seq scrna-seq seurat signac
Language:HTML 1

scatac-seq

zhanghao-njmu / SCP

liulab-dfci / MAESTRO

scverse / muon

pinellolab / STREAM

sanderlab / scPerturb

parashardhapola / scarf

sankaranlab / SCAVENGE

alexisvdb / singleCellHaystack

genecell / COSGR

aertslab / CREsted

shiquan / PISA

wukevin / babel

HaojiaWu / CellScopes.jl

swaruplabUCI / ArchRtoSignac

aertslab / single_cell_toolkit

pinellolab / pychromVAR

jumphone / BEER

caleblareau / mtscATACpaper_reproducibility

biobenkj / compartmap

mvinyard / ArchR-h5ad

AllenInstitute / aifi-swanson-teaseq

csbg / neuroblastoma

SUwonglab / sc-compReg

aertslab / scatac_fragment_tools

AprilYuge / ATAC-annotation-benchmark

bowang-lab / simATAC

raevskymichail / epi-impute

shuzwang / P2_cochlea

Barski-lab / sc-seq-analysis

gtca / chame

jumphone / InferLoop

cfusterot / scASAP

hyunsoo77 / maleBC_single_cells

lab-conrad / resVAE-ensemble

csbg / fibroblast-perturb-seq-analysis

manishabarse / scATAC-seq-and-scRNA-seq-Integration-Analysis-in-Adult-Mouse-Brain