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/hicproraw-to-bedpe
Import HiC-Pro raw matrix of any resolution into R and generate a hicexp object
hreypar/containers_test
Test running rules in a container
hreypar/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.
hreypar/felicidades
Repositorio para darle un pastel de cumpleaños a tus amix
hreypar/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
hreypar/mk-hicpro-validpairs
Run the HiC-Pro pipeline alignment, filtering and QC steps to obtain validPairs files for each pair of FASTQ files
hreypar/bedpe-to-hicexp
Import bedpe matrices of any resolution into R and generate a hicexp object
hreypar/circlize-DIRs
Use the Circlize package to visualise Hi-C DIRs in each human chromosome.
hreypar/ERCC1-phenotypes
hreypar/glm-hicexp
Obtain differentially interacting regions using glm methods to test a normalized hicexp object
hreypar/filter-hicexp-results
Filter a normalized and compared (difference detection) hicexp object
hreypar/get-DIRs-genes
Obtain the set of genes within genomic regions that present differential Hi-C interactions (according to multiHiCcompare)
hreypar/misc-codes-lcg
Codes from school times.
hreypar/mk-hicup-deduplicater
Run the HiCUP deduplicater on filtered SAM alignments to remove PCR duplicate read pairs
hreypar/mk-hicup-filter
Run the HiCUP filter on aligned SAM files to remove uninformative read pairs
hreypar/mk-trimmomatic
hreypar/multi-resolution-MCF10-DIRs
Compare Differentially Interacting Regions accross multiple resolutions.
hreypar/normalize-hicexp
Normalize Hi-C matrices from different conditions and with replicates using multiHiCCompare
hreypar/radian
A 21 century R console
hreypar/reychocolate2
La historia completa
hreypar/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
hreypar/sceasy
A package to help convert different single-cell data formats to each other
hreypar/snake-gtex-aracne
This repository is about downloading RNA-seq data samples from the GTEx project and parsing them into an annotated matrix
hreypar/snake-hic-diff
hreypar/stellarscope_figure_2
Stellarscope paper figure 2
hreypar/taller.supercomputo.inmegen
Repository with material from the Supercomputing Course-Workshop at INMEGEN
hreypar/tcga_basal_MInetwork
Workflow to run ARACNe-AP on TCGA's basal and control samples
hreypar/templates
hreypar/test_NCHG
Test from contacts to network using NCHG
hreypar/timeliner
a timeline about