Maxime Borry's starred repositories
annotated_deep_learning_paper_implementations
๐งโ๐ซ 60 Implementations/tutorials of deep learning papers with side-by-side notes ๐; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), gans(cyclegan, stylegan2, ...), ๐ฎ reinforcement learning (ppo, dqn), capsnet, distillation, ... ๐ง
firefox-translations
Firefox Translations is a webextension that enables client side translations for web browsers.
patchworklib
Patchwork for matplotlib: A subplot manager for intuitive layouts in matplotlib, seaborn, and plotnine.
vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
parasail-python
Python bindings for the parasail C library.
pr2database
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
pytaxonkit
Python bindings for the TaxonKit library
pathPhynder
A workflow for integrating ancient lineages into present-day phylogenies.
Wallen_DAMethodCompare_2021
Repository for data and code used in the manuscript "Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing"
TransforKmers
[WIP] A task-agnostic facility to pretrain/finetune/use a Transformer based model to classify your biological sequences.