Ahmed El Hosseiny's repositories
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
AcRanker
AcRanker is a machine learning system developed in python that ranks proteins in a proteome as per their Anti-CRISPR tendencies predicted using sequence features.
autofastq
script to automate Illumina bcl2fastq utility
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics-toolbox
Docker container for bioinformatics tools and pipelines
bioinformatics-workbook
Bioinformatics Workbook repository
eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
IRkernel
R kernel for Jupyter
kent
UCSC Genome Browser source tree. Stable branch: "beta".
miEAA-API
API and package code for miEAA 2.0
plink-ng
A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
speciationgenomics.github.io
Repository for speciation genomics website
TF_enrichment_analysis
COVIDomics paper: Transcription factor activity network
tidycovid19
{tidycovid19}: An R Package to Download, Tidy and Visualize Covid-19 Related Data
weka-wiki
Home of the Weka wiki.
Wochenende
A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3