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Bioconductor packages

Doc 📘 Bioconductor 🧬 Bioc builds ⚙️ Github 📦 Github checks 🧾 Lifecycle 🍃
Doc tidyCoverage Bioc release:
Release
Bioc devel:
Devel		 tidyCoverage rworkflows
Doc plyinteractions Bioc release:
Release
Bioc devel:
Devel		 plyinteractions rworkflows
Doc OHCA Bioc release
Bioc devel		 OHCA rworkflows
Doc BiocBook Bioc release:
Release
Bioc devel:
Devel		 BiocBook rworkflows
Doc HiCExperiment Bioc release:
Release
Bioc devel:
Devel		 HiCExperiment rworkflows
Doc HiContacts Bioc release:
Release
Bioc devel:
Devel		 HiContacts rworkflows
Doc HiCool Bioc release:
Release
Bioc devel:
Devel		 HiCool rworkflows
Doc HiContactsData Bioc release:
Release
Bioc devel:
Devel		 HiContactsData R-CMD-check-bioc
Doc DNAZooData Bioc release:
Release
Bioc devel:
Devel		 DNAZooData rworkflows
Doc fourDNData Bioc release:
Release
Bioc devel:
Devel		 fourDNData rworkflows
Doc VplotR Bioc release:
Release
Bioc devel:
Devel		 VplotR rworkflows
Doc periodicDNA Bioc release:
Release
Bioc devel:
Devel		 periodicDNA -

Other resources

  • hicstuff: lightweight library/pipeline to generate and handle Hi-C data
  • metator: Metagenomic binning based on Hi-C data
  • tinyMapper: Versatile pipeline to process a variety of genome-wide assays
  • autobcl2fastq: Automatically fetch data from a remote sequencer directory, demultiplex fastq files, trim adaptors and run some preliminary QCs

Jacques Serizay's Projects

autobcl2fastq icon autobcl2fastq

Automatically fetch data from sequencer directory, process with with bcl2fastq and run some preliminary QCs

delayedarray icon delayedarray

A unified framework for working transparently with on-disk and in-memory array-like datasets

dnart icon dnart

dn&art: DNA Networks & Assisted Representation of Time

dnazoodata icon dnazoodata

Gateway package to DNA Zoo-provided Hi-C maps and genome assemblies

drugchoice icon drugchoice

Shiny app developed for the sudo:sequence Hackathon 2018 in Cambridge UK

ebi_multiomics_2020 icon ebi_multiomics_2020

Multi-omics data integration project designed and taught for the EMBL/EBI course: Introduction to Multiomics Data Integration and Visualisation (2020)

fastcluster icon fastcluster

Fast hierarchical clustering routines for R and Python.

fourdndata icon fourdndata

Gateway package to 4DN-provided Hi-C maps and derived genomic files

hicontacts icon hicontacts

Analyzing Hi-C data in R with HiCExperiment objects

hicool icon hicool

Processing Hi-C raw data within R

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