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allele-imbalance-analysis-of-rna-and-dna

Allele-specific analysis of RNA-seq and DNA-seq data

allele-specific-expression

Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)

allhic

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq

ase

early version of (Pipeline for detection of differential allelic imbalance from RNA-seq)

asereadcounter_star

Preprocessing sequencing data for allele-specific analysis

bulk-segregation-analysis

Developed by Qiaoshan Lin in Yaowu Yuan Lab

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

galbraith-2016-pnas-ase-replication

Replicating the bioinformatics and statistics pipelines for allele-specific expression analysis of ovary tissue from F1 honey bees of AHBxEHB reciprocal crosses as described in Galbraith et al. (2016). PNAS. https://www.pnas.org/content/113/4/1020

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

mimut

mutant identification in Mimulus lewisii complex

mutmap

MutMap pipeline to identify causative mutations responsible for a phenotype

my_wgcna

pseudogenization_and_resurrection_cb

Repository of the Current Biology publication: Pseudogenization and resurrection of a speciation gene

r-guides

This repository contains the codes for the R tutorials on statology.org

rnaseq

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

seqtk

Toolkit for processing sequences in FASTA/Q formats

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

training-prep-2015-09

Instructor training preparation, September 2015

verta_jones_elife_2019

Scripts used in analysis of "Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks".

wgcna_tutorial

A step-by-step tutorial for Weighted correlation network analysis (WGCNA)

wtdbg

A fuzzy Bruijn graph approach to long noisy reads assembly