Pinned Repositories
bedpe-to-hicexp
Import bedpe matrices of any resolution into R and generate a hicexp object
circlize-DIRs
Use the Circlize package to visualise Hi-C DIRs in each human chromosome.
containers_test
Test running rules in a container
export-hicproraw
This module finds the output HiC-Pro raw matrices (bed and matrix files) and creates a directory structure to be consumed by hicproraw-to-bedpe.
felicidades
Repositorio para darle un pastel de cumpleaños a tus amix
glm-hicexp
Obtain differentially interacting regions using glm methods to test a normalized hicexp object
hicproraw-to-bedpe
Import HiC-Pro raw matrix of any resolution into R and generate a hicexp object
mk-hicpro-validpairs
Run the HiC-Pro pipeline alignment, filtering and QC steps to obtain validPairs files for each pair of FASTQ files
mk-pdf-docs
convert markdown documents to PDF using a LaTeX template.
subset-fastq-files
Generate smaller FASTQ files by selecting a random number of reads from the originals
hreypar's Repositories
hreypar/download-sra
Use prefetch to download sra files and fasterq-dump to obtain FASTQ files from them
hreypar/mk-fastp
Run fastp under an mk framework
hreypar/mk-pdf-docs
convert markdown documents to PDF using a LaTeX template.
hreypar/subset-fastq-files
Generate smaller FASTQ files by selecting a random number of reads from the originals
hreypar/fastq-quality-check
Generate a FastQC report for each FASTQ file and a composite report using MultiQC
hreypar/HiC_data
A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
hreypar/misc-codes-mpi
A collection of Perl and R scripts that I have used in the past. ca 2013
hreypar/mk-hicup-mapper
Run the HiCUP mapper on truncated FASTQ files to obtain aligned SAM files
hreypar/mk-hicup-truncater
Run the HiCUP truncater script on raw FASTQ files to remove the ligation junction (and downstream) sequences from the reads