|
Python |
5 |
Single cell ATAC-Seq Snakemake pipeline |
Sep 25, 2021 |
|
R |
2 |
Analysis Pipeline for Single Cell ATAC-seq |
Jul 30, 2022 |
|
Jupyter Notebook |
4 |
Single cell ATAC-Seq preprocessing for single cell explorer |
May 29, 2021 |
|
Python |
2 |
Snakemake pipeline for processing single-cell combinatorial indexing ATAC seq data |
Oct 10, 2019 |
|
Jupyter Notebook |
140 |
Benchmarking computational single cell ATAC-seq methods |
Aug 11, 2022 |
|
Python |
2 |
4DN ATAC-seq pipeline, inherited from ENCODE ATAC-seq pipeline |
Oct 31, 2022 |
|
Python |
7 |
Single Cell RNA-seq Pipeline |
May 18, 2022 |
|
R |
4 |
A/B compartments from single-cell ATAC seq (scATAC) |
Aug 17, 2018 |
|
Python |
4 |
An interactive browser for single-cell ATAC-seq data |
Feb 10, 2022 |
|
R |
4 |
A single-cell ATAC-seq simulation framework (R package) |
Jan 04, 2023 |
|
Python |
270 |
ENCODE ATAC-seq pipeline |
Aug 16, 2022 |
|
Python |
64 |
ATAC-seq snakemake pipeline |
Oct 19, 2022 |
|
Python |
2 |
BSF ATAC-seq pipeline |
Dec 22, 2021 |
|
R |
3 |
A single-cell RNA-seq pipeline |
Apr 20, 2023 |
|
R |
3 |
Analysis of single-cell ATAC-seq data using topic models. |
Apr 06, 2023 |
|
HTML |
16 |
Python package for analysis of multiomic single cell RNA-seq and ATAC-seq. |
Apr 25, 2022 |
|
Python |
154 |
ATAC-seq and DNase-seq processing pipeline |
Apr 21, 2023 |
|
R |
7 |
Single cell RNA-seq and ATAC seq analysis of cardiac progenitor cell transition states and lineage … |
Oct 08, 2021 |
|
Python |
55 |
Analysis pipeline for ATAC-seq Data |
Apr 17, 2023 |
|
None |
13 |
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc. |
Dec 01, 2022 |
|
None |
3 |
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc. |
Jun 17, 2017 |
|
None |
4 |
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc. |
Oct 28, 2018 |
|
Python |
5 |
Milne Lab ChIP-seq, ATAC-seq and RNA-seq pipeline |
Mar 31, 2023 |
|
R |
9 |
Repository for CCBR single cell RNA-Seq pipeline |
Jun 16, 2022 |
|
HTML |
2 |
Test data for ENCODE atac-seq-pipeline |
Dec 04, 2019 |
|
HTML |
2 |
Nextflow pipeline for ATAC-seq data analysis |
Feb 04, 2023 |
|
Shell |
2 |
cwl implementation of the ATAC-seq pipeline |
Feb 04, 2020 |
|
Nextflow |
17 |
Pipeline for Universal Mapping of ATAC-seq |
Aug 21, 2023 |
|
Groovy |
3 |
A Nextflow pipeline for single-cell RNA-Seq dataset |
Apr 21, 2024 |
|
Python |
19 |
Bead-based single-cell atac processing |
Jul 20, 2022 |
|
Shell |
2 |
MoTrPAC implementation of the ENCODE ATAC-seq pipeline |
Feb 12, 2024 |
|
None |
2506 |
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. |
May 12, 2023 |
|
Jupyter Notebook |
2 |
single-cell RNA-seq |
Mar 28, 2023 |
|
Python |
3 |
cell-free ChIP-seq pipeline |
Nov 28, 2022 |
|
Jupyter Notebook |
2 |
Pipeline for assembling TCRs from single-cell RNA-seq with TRACER |
May 15, 2021 |
|
Nextflow |
114 |
ATAC-seq peak-calling, QC and differential analysis pipeline |
Aug 15, 2022 |
|
Python |
3 |
The ENCODE DCC ATAC-seq pipeline, adapted for Krews |
Dec 24, 2020 |
|
R |
42 |
A modular, containerized pipeline for ATAC-seq data processing |
Mar 28, 2023 |
|
R |
4 |
Single Cell Pipeline |
Aug 19, 2022 |
|
Shell |
2 |
Single Cell RNA-Seq Imputation |
Mar 31, 2021 |
|
Python |
2 |
Single cell RNA-seq tools |
Jul 20, 2022 |
|
Python |
4 |
single-cell RNA-seq clustering |
Jul 27, 2021 |
|
HTML |
18 |
scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data |
May 14, 2023 |
|
R |
9 |
A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq) |
May 23, 2022 |
|
C++ |
72 |
Pipeline for initial analysis of droplet-based single-cell RNA-seq data |
Jul 07, 2022 |
|
R |
14 |
Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks |
Oct 28, 2022 |
|
HTML |
2 |
Cluster single cell RNA-seq data |
Sep 30, 2020 |
|
Rust |
41 |
Single-Cell RNA-seq pseudo-aligner |
Mar 22, 2023 |
|
R |
22 |
Single cell RNA-seq analysis bundle |
Mar 28, 2023 |
|
HTML |
14 |
Cellular Genetics Informatics Notebooks |
Feb 28, 2023 |