GatorShan

GatorShan's Stars

• alexdobin/STAR

  RNA-seq aligner

  Language:C1.9k842.1k508

• trinityrnaseq/trinityrnaseq

  Trinity RNA-Seq de novo transcriptome assembly

  Language:Perl841571.4k320

• freebayes/freebayes

  Bayesian haplotype-based genetic polymorphism discovery and genotyping.

  Language:C++79646692264

• davidemms/OrthoFinder

  Phylogenetic orthology inference for comparative genomics

  Language:Python72827923189

• biod/sambamba

  Tools for working with SAM/BAM data

  Language:D57427458107

• vcftools/vcftools

  A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

  Language:C++50932193148

• FelixKrueger/TrimGalore

  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

  Language:Perl47921177150

• FelixKrueger/Bismark

  A tool to map bisulfite converted sequence reads and determine cytosine methylation states

  Language:HTML40014654103

• hbctraining/DGE_workshop

  Language:HTML3762233164

• yupenghe/methylpy

  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

  Language:Python13749047

• hahnlab/CAFE5

  Version 5 of the CAFE phylogenetics software

  Language:C++117714022

• Oshlack/Lace

  Building SuperTranscripts: A linear representation of transcriptome data

  Language:Python67113919

• juliema/aTRAM

  Language:Python36725214

• irusri/Extract-intron-from-gff3

  This script will extract the intron feature gff3 and sequence from gene_exon gff3 and fasta file.

  Language:Perl333511

• Wendellab/CisTransRegulation

  Project description and analytic scripts for cis/trans regulation of fiber development in G. hirsutum

  Language:R161247

• bioinfogenome/GSP

  A tool for Genome Specific Primers design in polyploid species

  Language:C++7222

• niederhuth/Replaying-the-evolutionary-tape-to-investigate-subgenome-dominance

  DNA methylation scripts for the paper: Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

  Language:Python6101

• Wendellab/homoeologGeneExpression-Coexpression

  Challenges and pitfall in the use of partitioned gene counts for homoeologous gene expression and co-expression network analyses

  Language:R6413

• andrechanderbali/Buxus-Tetracentron-Genomes

  Repository of scripts and command-line agruments used in the manuscript "Buxus and Tetracentron genomes help resolve eudicot genome history"

  Language:Perl5100

• niederhuth/Widespread-natural-variation-of-DNA-methylation-within-angiosperms

  Data and scripts for Widespread natural variation of DNA methylation within angiosperms

  Language:Python5103

• BBarbazukLab/papers

  Repository containing all scripts and documentation for published papers.

  Language:HTML3104

• EvoEpi/python

  A collection of Python scripts for handling various data files.

  Language:Python3100

• bhofmei/analysis-scripts

  personal scripts used for data analysis and image making

  Language:Python2211

• kaseykhanhpham/nitfix-annotation

  documentation on annotation pipeline for NSF Nitfix project long read genome assemblies

  Language:Python2100

• LeiYang-Fish/copyseparator-v1.0.0-old-version

  Assembling Long Gene Copies from Short Read Data

  Language:R2100