Balharbi

bgee_pipeline

Source code of the Bgee pipeline

dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

genomation

R package for genomic feature analysis and visualization

methylation_scripts

All methylation file handling/processing scripts I ever made

recount3-docs

Documentation for all things related to `recount3`

SomeRecords

Some very useful records for me.

Alzheimers_DNAm

Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls

bag-excel-scraper

An R script to download the BAG Excel file on COVID19, transform the data and bring it into the target data model. Quickly mashed together for @rob_salzer: https://twitter.com/rob_salzer/status/1245054668914470913

bioconda-utils

Utilities for building and managing bioconda recipes

bisulfite-seq-data-analysis-pipeline

This repo contains details of Bisulfite Processing Pipeline

book

ClusterProfShinyGSEA

A web-based application to perform Gene Set Enrichment Analysis (GSEA) using clusterProfiler and shiny R libraries

data_reporting

Script for visualising and reporting data

DMRichR

An executable and package for the statistical analysis and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

epuRate

A clean R Markdown template for your reports

fluentGenomics

plyranges and tximeta case study

GenomicDistributionsData

Data for GenomicDistributions R package

jaffelab

R package with commonly used functions by the Jaffe lab

janitor

simple tools for data cleaning in R

labs

Rmd source files for the HarvardX series PH525x

Machine-Learning-with-Python

Practice and tutorial-style notebooks covering wide variety of machine learning techniques

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

pacman

A package management tools for R

reghelper

R package with regression helper functions

rrbs-pipeline

A Snakemake pipeline for RRBS data analysis

splicejam

Sashimi plots for RNA-seq data using detected transcripts

swan_vis

A Python library to visualize and analyze long-read transcriptomes

systemPipeR

Project Website:

testdata

test.set

Till.i.Emerge.Modular

A collections of different biological for testing modules and