mandyzhang6's repositories
atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
bio_tools
Useful bioinformatic scripts
Brassica_oleracea_rapa_napus_code
Code for the Brassica oleracea/rapa/napus genomic comparison
circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
CisTransRegulation
Project description and analytic scripts for cis/trans regulation of fiber development in G. hirsutum
CleaveLand4
CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets
DemographicInference
Scripts to compare models of divergence using diffusion approximation (dadi)
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
gwas
UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
hic
Analysis of Chromosome Conformation Capture data (Hi-C)
jarad.github.com
Github userpage
LTRpred
De novo annotation of young and intact retrotransposons
methylKit
R package for DNA methylation analysis
methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
NAM-genomes
Detailed bioinformatics scripts and methods used in the NAM genome paper.
pangenome
Renders a collection of sequences into a pangenome graph.
pyflow-ChIPseq
a snakemake pipeline to process ChIP-seq files from GEO or in-house
rbook
Source files for "Learning Statistics with R"
RNA-seq-analysis
RNAseq analysis notes from Ming Tang
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
smallrnaseq
small rna-seq analysis package
smrnaseq
A small-RNA sequencing analysis pipeline
SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
statistics
An open statistics textbook for Psychology undergraduates