🧑‍🏫 60+ Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), ga…

Python SDK, Proxy Server (AI Gateway) to call 100+ LLM APIs in OpenAI (or native) format, with cost tracking, guardrails, loadbalancing and logging. [Bedrock, Azure, OpenAI, VertexAI, Cohere, Anthr…

Topic Modelling for Humans

Gene Set Enrichment Analysis in Python

Nimfa: Nonnegative matrix factorization in Python

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

Compressed sequence string module for Python

A pipeline for the identification of fungi in public metagenomics datasets

Data and the co-authored network I extracted for lab selection in 3D genome research field

Count number of mapped reads per reference in SAM files (often for RNA-Seq experiments)

Unorganized collection of bioinformatics scripts and utilities

A efficient peak finder for high coverage ChIP-seq experiments, written in python.

Collection of stand-alone tools

Code for the MLPP method described in: "Co-evolution based machine-learning for predicting functional interactions between human genes" Stupp et al.

Manuiplations and statistics on genomic data

some general useful python tools for genomics

Count number of mapped reads per reference in SAM files (often for RNA-Seq experiments)

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

RNASEQR - A streamlined and accurate RNA-seq sequence analysis program

MISO

PySeq is a python module that finds groups of items that follow a naming convention containing a numerical sequence index (e.g. fileA.001.png, fileA.002.png, fileA.003.png...) and serializes them i…

python package for working with immune receptor sequence data

Analysis tools for PhIP-seq experiments

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data