Astrid Deschênes's repositories
similaRpeak
Bioconductor Package - Metrics to estimate the level of similarity between two ChIP-Seq profiles
enrichViewNet
From functional enrichment results to biological networks
SignatureHeatmap
R package to create heatmaps using signature gene list and transcriptomic data
arcasHLATools
Tools to easy the extraction and manipulation of HLA typing produced by arcasHLA software
consensusSeekeR
This R package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. Tested on ChIP-Seq peaks and nucleosome positions.
docker-arcasHLA
Docker image for arcasHLA software
HLAClustRView
R package specialized in HLA typing clustering and visualization based on specific similarity metrics.
methInheritSim
Bioconductor Package - Whole-Genome Inherited Bisulphite Sequencing Data Simulation
methylInheritance
Bioconductor Package - Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
nucleoSimShiny
Interactive generation of nucleosomes maps using Shiny framework and based on Bioconductor nucleoSim package
RJMCMCNucleosomes
Bioconductor Package - Genome-Wide Nucleosome Positioning in R with an optimized section in C++
CNprep_test
CNprep — Pre-process DNA Copy Number (CN) Data for Detection of CN Events
CNVMetrics
R Package to compare copy number variant (CNV) results from multiple samples or methods
datasharing
The Leek group guide to data sharing
ExData_Plotting1
Plotting Assignment 1 for Exploratory Data Analysis
GeneiASE_Tools
R scripts to process input/output related to GeneiASE software
GettingandCleaningData
Getting and Cleaning Data Project
learningSlidify
This repo is mainly for leaning slidify from cousera course Data Science
MachineLearningWeightLifting
Qualitative Activity Recognition of Barbell Lifting Exercises
mpileupTools
This python script parses a mpileup file to extract the coverage of each base at each position.
OrganoidsToolBox
Enabling organoid analyses using drug sreening, RNA-seq, exome-seq
PairedPermutationTest
R package to carry out permutation tests on paired observations