scatac-seq
There are 49 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.
liulab-dfci/MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
scverse/muon
muon is a multimodal omics Python framework
pinellolab/STREAM
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
sanderlab/scPerturb
scPerturb: A resource and a python/R tool for single-cell perturbation data
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.
sankaranlab/SCAVENGE
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
alexisvdb/singleCellHaystack
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
genecell/COSGR
Accurate and fast cell marker gene identification with COSG
shiquan/PISA
A collection of tools to process single-cell omics datasets.
wukevin/babel
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
swaruplabUCI/ArchRtoSignac
An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
HaojiaWu/CellScopes.jl
A Julia package for single cell and spatial data analysis
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.
pinellolab/pychromVAR
A python package for chromVAR
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.
jumphone/BEER
BEER: Batch EffEct Remover for single-cell data
caleblareau/mtscATACpaper_reproducibility
Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
biobenkj/compartmap
Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
mvinyard/ArchR-h5ad
Parse ArchR arrow files to anndata h5ad
AllenInstitute/aifi-swanson-teaseq
Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization
csbg/neuroblastoma
Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis
SUwonglab/sc-compReg
R package for single-cell comparative regulatory analysis
aertslab/scatac_fragment_tools
Tools for working with scATAC-seq fragment files
AprilYuge/ATAC-annotation-benchmark
scripts for manuscript 'benchmarking automated cell type annotation tools for single-cell ATAC-seq data'
bowang-lab/simATAC
A single-cell ATAC-seq simulation framework (R package)
raevskymichail/epi-impute
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
shuzwang/P2_cochlea
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
Barski-lab/sc-seq-analysis
CWL toolkit for single-cell sequencing data analysis
gtca/chame
Chromatin analysis module
jumphone/InferLoop
InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop
cfusterot/scASAP
single-cell ATAC Sequencing Analysis Pipeline
hyunsoo77/maleBC_single_cells
This repository is for male breast cancer scRNA-seq and scATAC-seq data processing and figure generation.
lab-conrad/resVAE-ensemble
resVAE-ensemble: feature identification in single-cell data
csbg/fibroblast-perturb-seq-analysis
Epigenetic regulators of fibrotic transformation in cardiac fibroblasts