shenlab-sinai/pipelines_for_ChIP-seq_analysis

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Created almost 10 years ago
Updated almost 10 years ago

shenlab-sinai/pipelines_for_ChIP-seq_analysis

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Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

diffreps

Differential analysis for ChIP-seq with biological replicates

chip-seq_preprocess

A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.

GeneOverlap

R package for testing and visualizing gene list overlaps

region_analysis

A python script used to annotate genomic intervals.

ngsplotdb

Genome databases generation pipeline for ngs.plot and region_analysis.

DeepRegFinder

DeepRegFinder is a deep learning based program used to identify DNA regulatory elements using ChIP-seq

SPEctRA

A Scalable Pipeline for RNA‬‬‬-seq Ana‬‬lysis

NGS-Data-Charmer

This repository hosts an automated NGS data analysis (RNA-seq and ChIP-seq) pipeline created using Snakemake.

diffRepeats

Quantify repeat element enrichment with next-generation sequencing data

Gene-Attributes

A shiny app that obtains the coordinates and description of an input gene list (Ensembl v90) using biomaRt package.

RRHO2

Optimized RRHO2

software-best-practice

The best software engineering practices to develop bioinformatic programs

miRNA_pipeline_for_miRanalyzer

A pipeline of miRNA by using miRanalyzer