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atac-seq-pipeline

ENCODE ATAC-seq pipeline

atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

chipseqfpro

ChIPSeqFPro (beta) is a script for full processing of ChIPSeq data starting from fastq files. It performs fastqc quality control, mapping to the human genome hg19 or mouse mm10 using bwa, sam to bam conversion, peak calling with MACS, creates bigwig files from bam files using bam2bigwig.

count2fpkm

This Scirpt is used to transform the Read Count to FPKM by using DESeq2

diabetes-prediction

Predict Diabetes using Machine Learning.

dna-me-pipeline

DCC/DAC methylation pipeline source

dnbelab_c_series_scrna-analysis-software

An open source and flexible pipeline to analyze DNBelab C Series single-cell RNA datasets.

drop-seq

Java tools for analyzing Drop-seq data

dropest

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

dynamo-release

Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

eccdna_rca_nanopore

eccDNA identification from nanopore long reads of rolling-circle amplicon

gatk

Official code repository for GATK versions 4 and up

gene_signature

Clear cell Renal cell carcinoma is a type of kidney cancer which comprises the majority of all renal cell carcinomas. Many efforts have been made to identify biomarkers which could help healthcare professionals better treat this kind of cancer. With extensive public data available, we conducted a machine learning study to determine a gene signature

m6a-seq_analysis_workflow

A pipeline to process m6A-seq data and down stream analysis.

m6amethylation

m(6)A methylation analysis

macsr

MACS3 R/BioC wrapper

mageckflute

Integrative analysis pipeline for pooled CRISPR functional genetic screens

merip_reanalysis_scripts

Scripts for paper entitled "Limits in the detection of m6A changes using MeRIP/m6A-seq

methylkit

R package for DNA methylation analysis

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

my_wgcna

orthologr

Genome wide orthology inference and dNdS estimation

pisa

a preprocessing tool for single molecular data analysis

predicting-age-from-the-transcriptome-of-human-dermal-fibroblasts

Code to generate Figure 2 of the paper "Predicting age from the transcriptome of human dermal fibroblasts" from the FPKM tables

pyscenic

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

rmats2sashimiplot

rna-seq-slamseq

Snakemake workflow for slamDunk toolkit

rna-seq_analysis

scripts for RNA-Seq analysis

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.