Luca Cozzuto's repositories
tutorial-template
Template for the Read the Docs tutorial
redgrease
Grease for your Redis Gears
course_2021
my pipeline
test_course
just a test
sphinx-pages
Build html documentation by Sphinx, and push to branch gh-pages.
covid_stuff
some script for making plots
riboflow
Pipeline for Ribosome Profiling Data
covid_plots
Scripts for making plots
ThermoRawFileParser
Thermo RAW file parser that runs on Linux with mono
deeplexicon
Signal based nanopore RNA demultiplexing with convolutional neural networks
DEQ
An R package to conveniently run DESeq2, edgeR, and QNB for the detection of differential methylation in MeRIP/m6A-seq data.
tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
nextflow
Translating Nextflow in PhP
NF_test_case
nextflow test pipeline
Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data
chipseq
Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.
MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
FlowBio
A fast, easy way to present complex bioinformatics pipelines to biologists
SUPPA
SUPPA2: Fast quantification of differential splicing
millidocs
A simple documentation theme for Jekyll.
BioNextflow
Nextflow functions for biological tools
dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
docker-centos-perlbrew
Basic Docker image for running CentOS with perlbrew installed
indrops
Pipeline for processing inDrops sequencing data