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atacseq

ATAC-seq peak-calling and QC analysis pipeline

awesome-ggplot2

A curated list of awesome ggplot2 tutorials, packages etc.

bioinf2019

bioinfo-notebook

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

bioinformatics-cafe

Unsorted scripts for bioinformatics

bioscripts

Scripts for bioinformatics data processing and analysis

bottomup-ggm-semi-partial-corr

Gaussian Graphical Model based Gene Regulatory Network Construction from Gene Expression Data

broad-prod-wgs-germline-snps-indels

Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline

chia-pet2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data

chipseq

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

circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

cisd

Chromatin Interaction Site Detector

danpos3

Updated DANPOS2 to work with python3

dyngenie3

Semi-parametric approach for the inference of gene regulatory networks from time series of expression data

grid-seq

Scripts for GRID-seq analysis

gwas

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

hybrid-sequencing-workflow

This code is for processing the hybrid sequencing data from maize, utilizing the RNA-seq data to correct and check the whole chain of splicing junction of reads identified in PacBio-sequencing.

intro-to-chipseq

Intro to ChIPseq using HPC

iso-seq

iso-seq-tools

isoseq

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

isoseq3_stickleback

isoseqnat

Construct full-length transcriptome and identify Natural sense-Antisense Transcript pairs by PacBio Isoform Sequencing (Iso-Seq) data

jrmgrn

Joint reconstruction of multiple gene regulatory networks with common hub genes

learn-regex

Learn regex the easy way

lncpipe

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

lncrna_gb

new version of lncRNA using updated reference

lpanetwork

Using unsupervised machine learning methods to infer gene regulatory networks from expression data of low phytic acid soybean seeds.

maize_tissue-specific_grn

The repository source code for maize tissue-specific GRN project