pkhoueiry's repositories
pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
Attend-and-Excite
Official Implementation for "Attend-and-Excite: Attention-Based Semantic Guidance for Text-to-Image Diffusion Models"
BicPCA
Select the number of PCs using the Bayesian Information Criterion
wes_germline_gatk
GATK workflow for WES on germline samples
wes_somatic_gatk
GATK based WES workflow for somatic samples
cellxgene-gateway
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
cellxgene_VIP
Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
DNA-Sequence-Machine-learning
Understand DNA structure and how machine learning can be used to work with DNA sequence data.
dogmap
pipeline for dog WGS alignment
EnrichedHeatmap
make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
giskard
The testing framework dedicated to ML models, from tabular to LLMs 🛡️🧑🔬
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
TheAlgorithms
All Algorithms implemented in Python
trackplot
trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.