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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

download-sra

Use prefetch to download sra files and fasterq-dump to obtain FASTQ files from them

ercc1-phenotypes

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.

fastq-quality-check

Generate a FastQC report for each FASTQ file and a composite report using MultiQC

felicidades

Repositorio para darle un pastel de cumpleaños a tus amix

filter-hicexp-results

Filter a normalized and compared (difference detection) hicexp object

get-dirs-genes

Obtain the set of genes within genomic regions that present differential Hi-C interactions (according to multiHiCcompare)

glm-hicexp

Obtain differentially interacting regions using glm methods to test a normalized hicexp object

hic_data

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

hicproraw-to-bedpe

Import HiC-Pro raw matrix of any resolution into R and generate a hicexp object

misc-codes-lcg

Codes from school times.

misc-codes-mpi

A collection of Perl and R scripts that I have used in the past. ca 2013

mk-fastp

Run fastp under an mk framework

mk-hicpro-contact-maps

Place al the `validPairs` files corresponding to a replicate under the same directory and build a contact map per sample using HiC-Pro

mk-hicpro-validpairs

Run the HiC-Pro pipeline alignment, filtering and QC steps to obtain validPairs files for each pair of FASTQ files

mk-hicup-deduplicater

Run the HiCUP deduplicater on filtered SAM alignments to remove PCR duplicate read pairs

mk-hicup-filter

Run the HiCUP filter on aligned SAM files to remove uninformative read pairs

mk-hicup-mapper

Run the HiCUP mapper on truncated FASTQ files to obtain aligned SAM files

mk-hicup-truncater

Run the HiCUP truncater script on raw FASTQ files to remove the ligation junction (and downstream) sequences from the reads

mk-pdf-docs

convert markdown documents to PDF using a LaTeX template.

mk-trimmomatic

multi-resolution-mcf10-dirs

Compare Differentially Interacting Regions accross multiple resolutions.

normalize-hicexp

Normalize Hi-C matrices from different conditions and with replicates using multiHiCCompare

radian

A 21 century R console

reychocolate2

La historia completa

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

sceasy

A package to help convert different single-cell data formats to each other