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.github

The UAB Biological Data Science Core (U-BDS) is a UAB institutional resource which aims provide services, foster long-term collaborations with the UAB research community, and provide training for biomedical investigators on a specific set of analysis tools and techniques.

2d-spot-plot

2D Spot plot

academicons

LaTeX academicons package for high qual­ity icons of on­line aca­demic pro­files.

alphafold_pytorch

An implementation of the DeepMind's AlphaFold based on PyTorch for research

appyter-catalog

A catalog of appyter notebooks

awesome-deep-learning

A curated list of awesome Deep Learning tutorials, projects and communities.

awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

awesome-github-profile-readme

😎 A curated list of awesome GitHub Profile READMEs 📝

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bds_rstudio_template

Template OOD app for using BDS's RStudio Singularity app

beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

benchmarking-gnns

Repository for benchmarking graph neural networks

bert-enhancer

A Transformer Architecture Based on BERT and 2D Convolutional Neural Network to Identify DNA Enhancers from Sequence Information

bert-gen

bertviz

Tool for visualizing attention in the Transformer model (BERT, GPT-2, Albert, XLNet, RoBERTa, CTRL, etc.)

bioinfo_scripts

bioinformatics

Bioinformatics scripts

bioperl-pise

Original Pise-based wrappers for BioPerl (obsolete)

biopig

bitmab2-tutorials

Workshop materials for the Second Benthic Invertebrates, Metagenomics, and Bioinformatics Workshop at the TAMUCC Harte Institute in Corpus Christi, TX (January 15-19, 2018)

breakdancer

SV detection from paired end reads mapping

caffe

Caffe: a fast open framework for deep learning.

caffe2

Caffe2 is a lightweight, modular, and scalable deep learning framework.

calc-roi-covg

Given two BAM files, a reference sequence, and regions of interest, count the AT, CG, or CpG sites with sufficient read-depth in both BAMs.

centralitycosdist

civet

cmds

Cohort DNA Copy Number Analysis

copynumbr

An R package for copy number data (aCGH, SNP arrays)

coursera-machine-learning

source from exercises in Coursera.

csv_to_json

Converting hierarchical data stored in csv like file to python dict/json