|
Python |
154 |
ATAC-seq and DNase-seq processing pipeline |
Apr 21, 2023 |
|
Python |
5 |
Milne Lab ChIP-seq, ATAC-seq and RNA-seq pipeline |
Mar 31, 2023 |
|
Shell |
2 |
Hashed scRNA-seq data processing pipeline |
Mar 30, 2022 |
|
wdl |
4 |
ENCODE DNase-seq pipeline |
Feb 28, 2021 |
|
Python |
3 |
scNavigator processing pipeline for scRNA-seq data |
Aug 16, 2023 |
|
R |
6 |
One liner analyses and visualizations for bulk RNA-seq and ChIP-seq data |
Aug 10, 2022 |
|
Python |
3 |
DNase I seq QC pipeline |
Nov 17, 2017 |
|
R |
91 |
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets |
Apr 11, 2023 |
|
R |
10 |
Processing scRNA-seq data with kallisto|bustools pipeline |
Dec 08, 2022 |
|
R |
9 |
A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq) |
May 23, 2022 |
|
HTML |
2 |
script for RNA-seq and Chip-seq |
Apr 17, 2021 |
|
Python |
106 |
ENCODE Uniform processing pipeline for ChIP-seq |
Jun 08, 2022 |
|
Python |
2 |
ENCODE Uniform processing pipeline for ChIP-seq |
Sep 07, 2022 |
|
Python |
20 |
Bulk RNA-seq analysis. |
Aug 07, 2022 |
|
Python |
3 |
RNA-Seq pipeline |
May 04, 2021 |
|
Python |
84 |
STAR based ENCODE Long RNA-Seq processing pipeline |
Jun 24, 2022 |
|
Python |
3 |
CITE-seq pipeline using Salmon and Alevin (HuBMAP scRNA-seq pipeline) |
Apr 14, 2023 |
|
Python |
2 |
Benzimidazole RNA-Seq and smRNA-Seq Pipeline |
May 28, 2020 |
|
HTML |
36 |
Introduction to bulk RNA-seq |
Aug 08, 2022 |
|
Shell |
4 |
RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @Cornell-Trex |
Oct 14, 2021 |
|
Python |
2 |
RNA-Seq NGS Pipeline |
Feb 21, 2023 |
|
Python |
3 |
RNA seq analysis pipeline |
Nov 07, 2022 |
|
Python |
183 |
ENCODE ChIP-seq pipeline |
Aug 11, 2022 |
|
HTML |
10 |
Self-guided educational workshop for ChIP-Seq and RNA-Seq |
Sep 19, 2022 |
|
R |
4 |
Scripts to analyze single-cell and bulk RNA & ChIP-seq of TNBC under drug treatment |
Mar 31, 2023 |
|
Python |
254 |
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA. |
Apr 26, 2023 |
|
Python |
3 |
This repository hosts an automated NGS data analysis (RNA-seq and ChIP-seq) pipeline created using Snakemake. |
Jan 23, 2023 |
|
Shell |
11 |
ENCODE DNase-seq pipeline essentials for running on dnanexus. |
Nov 07, 2019 |
|
Python |
7 |
Single Cell RNA-seq Pipeline |
May 18, 2022 |
|
Python |
3 |
scRNA-seq pipeline using Salmon for quantification |
Feb 08, 2022 |
|
R |
9 |
A pipeline for scRNA-seq data analysis |
Apr 04, 2023 |
|
Perl |
2 |
MARS-SEQ pipeline (scrna module from tlsrc) |
Nov 17, 2022 |
|
Java |
2 |
AQUAS TF ChIP-seq pipeline |
Jan 19, 2022 |
|
Python |
3 |
cell-free ChIP-seq pipeline |
Nov 28, 2022 |
|
Groovy |
6 |
Dalmolin Group's workflow for pre-processing, alignment and quantification of bulk RNA-seq data |
Dec 14, 2023 |
|
R |
9 |
RNA-seq, QC and differential analysis pipeline |
Aug 15, 2022 |
|
Python |
2 |
Prediction of RNA splicing kinetics in scRNA-seq data |
Apr 10, 2023 |
|
Python |
3 |
Snakemake workflow to analyze bulk RNA-seq |
Nov 08, 2022 |
|
Shell |
9 |
Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq … |
Sep 14, 2022 |
|
Java |
102 |
AQUAS TF and histone ChIP-seq pipeline |
Mar 13, 2023 |
|
Shell |
2 |
Pipeline for gecco RNA-seq analysis |
Oct 05, 2021 |
|
Perl |
2 |
Nextflow based RNA-seq analysis pipeline |
Nov 19, 2021 |
|
wdl |
26 |
ENCODE long read RNA-seq pipeline |
Aug 09, 2022 |
|
R |
3 |
A single-cell RNA-seq pipeline |
Apr 20, 2023 |
|
Python |
25 |
Zavolan-Lab Automated RNA-Seq Pipeline |
Apr 10, 2023 |
|
Python |
5 |
Epitope discovery pipeline for RNA-seq |
Jan 25, 2020 |
|
Java |
10 |
Unix-based RNA-seq quantification pipeline |
Dec 01, 2021 |
|
R |
7 |
ChIP-Seq Pipeline implemented using Nextflow |
Jun 07, 2022 |
|
Python |
2 |
Technical ChIP-Seq pipeline on snakemake |
Jan 24, 2023 |
|
Perl |
4 |
A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments |
May 15, 2023 |