Pinned Repositories
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scripts
00_Pangenome_Analysis
Pangenome Analysis Workflow with Prodigal and CD-HIT
12-trees
Variants analysis
A188Ref1
the process to build the first A188 reference genome
Ab10-Assembly
B73Ab10 genome assembly methods
adapt_PurgeHaplotigs_for_FALCONPhase
Convert output of purge haplotigs to format compatible with FALCON-Phase
adaptiPhy
This computational method has been published in BMC genomics as: "Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral"
admixturePipeline
A pipeline that accepts a VCF file to run through Admixture
HiC_tools
A collection of tools for Hi-C data analysis
maf2synteny
A tool for recovering synteny blocks from multiple alignment
bioCKO's Repositories
bioCKO/PseudogenePipeline-1
Scripts and wrapper for runing the Shiu Lab's pseduogene pipeline.
bioCKO/Discover_pseudogenes
Discover pseudogenes in a newly assembled genome, using reference gene/protein sequences.
bioCKO/combine2contigs
bioCKO/Y-chromosome
bioCKO/pipelines
bioCKO/HaploMerger2
bioCKO/centromere_seeker
bash script to search for centromeric repeat patterns in PacBio data, using several current tools (trf and R)
bioCKO/finishingTool
finshingTool
bioCKO/sex-SNP-finder
bioCKO/allele-biased-expression
Guide to uncover parent-of-origin gene expression bias
bioCKO/HapSVAssembler
bioCKO/chain_filter
bioCKO/msoar2.0
MSOAR2.0 program
bioCKO/paper-xiong2016
bioCKO/DASVC
De-novo Assembly Structural Variant Caller
bioCKO/Nematoda-TE-Evolution
Analysis for the paper "Genetic drift, not life history or RNAi, determine long term evolution of transposable elements"
bioCKO/teleost_genomes_immune
bioCKO/snp_plotter
snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data.
bioCKO/GeneFamilyAnalysis
Compute gene families for a set of genomes.
bioCKO/KSPlotting
bioCKO/piRNAPredictor
source codes and datasets for paper ‘A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs’
bioCKO/dNdS_for_grunts
bioCKO/Anole_expression
Understanding variation in squamate sex determination and sex chromosome evolution
bioCKO/RES-Scanner
RES-Scanner is a software package for genome-wide identification and annotation of RNA-editing sites for any species with matched RNA-Seq and DNA-Seq data.
bioCKO/TE-search-tools
Python wrappers for programs that search for transposable elements
bioCKO/science
bioCKO/genome-rearrangements
bioCKO/presentations
Bring Your Own Bioinformatics
bioCKO/cytoscape_files_generator
bioCKO/PARdiversity