analogiks's repositories
RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
BERN2
BERN2: an advanced neural biomedical namedentity recognition and normalization tool
DataProfiler
What's in your data? Extract schema, statistics and entities from datasets
samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
AEGIS
MHC-II presentation predictor
mudskipper
A tool for projecting genomic alignments to transcriptomic coordinates
bigmhc
BigMHC is a deep learning tool for predicting MHC-I (neo)epitope presentation and immunogenicity
ffq
A tool to find sequencing data and metadata from public databases.
DeepImmuno
Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
DeepTCR
Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
pMTnet
Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
ProtTrans
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
gget
gget enables efficient querying of genomic databases, such as Ensembl, UniProt, NCBI, directly into a Python or terminal programming environment. It was designed to support genomic data analysis.
bowtie
An ultrafast memory-efficient short read aligner
MhcVizPipe
A reporting pipeline for visualization of immunopeptidomics MS data.
PRIME
PRedictor of IMmunogenic Epitopes
bio-transformers
bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.
pytorch-large-model-support
Large Model Support in PyTorch
emacs-python-black
Emacs package to reformat Python using black-macchiato
biopython
Official git repository for Biopython (originally converted from CVS)
tsnad
Detecting somatic mutations and predicting tumor-specific neo-antigens
TPMCalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
ecco
Visualize and explore NLP language models. Ecco creates interactive visualizations directly in Jupyter notebooks explaining the behavior of Transformer-based language models (like GPT2).
DeBERTa
The implementation of DeBERTa
hosts
Consolidating and extending hosts files from several well-curated sources. You can optionally pick extensions to block pornography, social media, and other categories.