Pinned Repositories
2018_Ecological_Genomics
The Spring 2018 Ecological Genomics course at the University of Vermont
abc_inferences
allele-specific-expression
Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)
ATAC-seq
atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
bio_tools
Useful bioinformatic scripts
bioinformatics_scripts
Just a bunch of scripts I use for bioinformatics -- feel free to use, reuse, and improve
book
Brassica-napus-genomes
docs
Documentation of the Snakemake-Workflows project
mandyzhang6's Repositories
mandyzhang6/abc_inferences
mandyzhang6/atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
mandyzhang6/bio_tools
Useful bioinformatic scripts
mandyzhang6/book
mandyzhang6/Brassica_oleracea_rapa_napus_code
Code for the Brassica oleracea/rapa/napus genomic comparison
mandyzhang6/circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
mandyzhang6/CisTransRegulation
Project description and analytic scripts for cis/trans regulation of fiber development in G. hirsutum
mandyzhang6/CleaveLand4
CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets
mandyzhang6/DemographicInference
Scripts to compare models of divergence using diffusion approximation (dadi)
mandyzhang6/gatk_haplotype
mandyzhang6/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
mandyzhang6/gwas
UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
mandyzhang6/hic
Analysis of Chromosome Conformation Capture data (Hi-C)
mandyzhang6/jarad.github.com
Github userpage
mandyzhang6/LDhat_workflow
mandyzhang6/LTRpred
De novo annotation of young and intact retrotransposons
mandyzhang6/methylKit
R package for DNA methylation analysis
mandyzhang6/methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
mandyzhang6/NAM-genomes
Detailed bioinformatics scripts and methods used in the NAM genome paper.
mandyzhang6/pangenome
Renders a collection of sequences into a pangenome graph.
mandyzhang6/pyflow-ChIPseq
a snakemake pipeline to process ChIP-seq files from GEO or in-house
mandyzhang6/rbook
Source files for "Learning Statistics with R"
mandyzhang6/RNA-seq-analysis
RNAseq analysis notes from Ming Tang
mandyzhang6/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
mandyzhang6/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
mandyzhang6/scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
mandyzhang6/smallrnaseq
small rna-seq analysis package
mandyzhang6/smrnaseq
A small-RNA sequencing analysis pipeline
mandyzhang6/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
mandyzhang6/statistics
An open statistics textbook for Psychology undergraduates