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/CD_RF_microbiome
Scripts for processing and analyzing the microbiome data associated with the manuscript "Multi-omics Differentially Classify Disease State and Treatment Outcome in Paediatric Crohn’s Disease"
bioCKO/lncRNA-1
bioCKO/positiveSelectionPipeline
Random perl and shell scripts plus notes for whole genome CDS positive selection detection
bioCKO/phasm
Haplotype-aware de novo genome assembly for polyploid organisms from long read data
bioCKO/RPASE
The package RPASE (Read-backed Phasing-based ASE detection) implements an algorithm for identifying genes which show allele-specific expression (ASE) on a per-individual and per-gene basis, using RNA-seq read count data.
bioCKO/miRNA_Project
miRNA Discovery Project : simple, easy-to-use, rule-based miRNA candidate discovery with multithread acceleration
bioCKO/CNVRepeat
bioCKO/HomolContigsByAnnotation
python script to identify genes that are present on multiple contigs
bioCKO/Genomic_Utilities
bioCKO/bin
some small script in bioinformatics
bioCKO/PythonNGSTools
Scripts for NGS processing
bioCKO/quota-alignment
Guided synteny alignment between duplicated genomes (within specified quota constraint)
bioCKO/HABOT2
Hybrid genome assembly using 2nd and 3rd generation sequencing data
bioCKO/Danaus_NeoZ-Public
Public repo for code related to discovery of NeoZ chromosome in Danaus butterflies
bioCKO/ASEtrans
Codes for allele specific expression
bioCKO/positive_selection
Tests for evidence of positive selection using anthozoan transcriptomes
bioCKO/rabbit-genome-assembler
bioCKO/SNPath
An R package for pathway analysis of GWAS data (SNPath)
bioCKO/s-plot
A simple plot library
bioCKO/SAPA
SNP annotation programm for AML
bioCKO/Pseudogene_v2
bioCKO/ASEofBases
Allele Specific Expression method and pipeline for analysis
bioCKO/Bioinf_utils
Phd backup of bioinf stuff
bioCKO/code4cos
bioCKO/custom_filtering_and_mutated_gene_annotation
Extension of filtering of somatic non-synonymous SNVs and INDELs (custom filtering strategy using samtools mpileup) followed by custom functional annotation of each variant and the gene they are mutated in.
bioCKO/CIRCpseudo
Pipeline for circRNA-derived pseudogenes
bioCKO/MiRCA
Hybrid Error Correction Tool for NGS Long Reads
bioCKO/RhesusLncRNA
bioCKO/lncRNA-screen
lncRNA-screen
bioCKO/PseudogenePipeline