Name: Nilesh Kumar (Ph.D)
Type: User
Company: University of Alabama at Birmingham
Bio: 🎓Bioinformatician III at the "Ircp-Biological Data Sciences"
Twitter: nilesh_uab
Location: 1720 University Blvd, Birmingham, AL 35294
Blog: https://scholars.uab.edu/13757-nilesh-kumar/publications
Nilesh Kumar (Ph.D)'s Projects
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
LaTeX academicons package for high quality icons of online academic profiles.
An implementation of the DeepMind's AlphaFold based on PyTorch for research
A catalog of appyter notebooks
A curated list of awesome Deep Learning tutorials, projects and communities.
A curated list of awesome deep learning applications in the field of computational biology
😎 A curated list of awesome GitHub Profile READMEs 📝
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Template OOD app for using BDS's RStudio Singularity app
BEELINE: evaluation of algorithms for gene regulatory network inference
Repository for benchmarking graph neural networks
A Transformer Architecture Based on BERT and 2D Convolutional Neural Network to Identify DNA Enhancers from Sequence Information
Tool for visualizing attention in the Transformer model (BERT, GPT-2, Albert, XLNet, RoBERTa, CTRL, etc.)
Bioinformatics scripts
Original Pise-based wrappers for BioPerl (obsolete)
Workshop materials for the Second Benthic Invertebrates, Metagenomics, and Bioinformatics Workshop at the TAMUCC Harte Institute in Corpus Christi, TX (January 15-19, 2018)
SV detection from paired end reads mapping
Workshop materials for the U-BDS bulk RNA-seq lessons
Caffe: a fast open framework for deep learning.
Caffe2 is a lightweight, modular, and scalable deep learning framework.
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.
Cohort DNA Copy Number Analysis
An R package for copy number data (aCGH, SNP arrays)
source from exercises in Coursera.