Pinned Repositories
acpi_call
A linux kernel module that enables calls to parameterless ACPI methods through /proc/acpi/call
bioboxes_playground
bumblebee
Optimus Support for Linux Through VirtualGL
calculate_clip_overlap
calculate rate of overlapping bases in paired-end reads from a bam file
developments-in-next-generation-sequencing
Developments in next generation sequencing: instruments, read lengths, throughput
ensembl-hive-sge
ensembl-hive
eutebi
tools for eutebi project
life-in-the-uk-test
pinball
pinball code
pubmode
PubMode - A PubMed interface for Emacs
avilella's Repositories
avilella/life-in-the-uk-test
avilella/ThermoMPNN
GNN trained to predict changes in thermodynamic stability for protein point mutants
avilella/utils
utils
avilella/alphafold_non_docker
AlphaFold2 non-docker setup
avilella/apq-qsne
A collection of code for Dimensionality Reduction for Documents with Nearest Neighbor Queries
avilella/awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
avilella/bhtsne
Barnes-Hut t-SNE
avilella/BLAZE
SingleCell Nanopore sequencing data analysis
avilella/ColabDesign
Making Protein Design accessible to all via Google Colab!
avilella/dandelion
dandelion - A single cell BCR-seq analysis package for 10X Chromium 5' data
avilella/DProQ
Deep learning prediction of protein complex structure quality
avilella/enclone
VDJ Clone Analysis Tools
avilella/folding_tools
A collection of *fold* tools
avilella/GraphBP
Official implementation of "Generating 3D Molecules for Target Protein Binding" [ICML2022 Long Presentation]
avilella/k-means
Simple k-means clustering implementation
avilella/kmeans
Implementation of the K-Means clustering algorithm.
avilella/LMNglyPred
Prediction of Human N-Linked Glycosylation Site using embeddings from pre-trained protein language model
avilella/mark-nonconverted-reads
This program examines a BAM or SAM stream for reads that contain multiple Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints summary information to stderr.
avilella/methylKit
R package for DNA methylation analysis
avilella/modPhred
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
avilella/nanoranger
simplified cellranger for long-read data
avilella/nf-bowtie
Align reads with bowtie to reference.
avilella/papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
avilella/pline
JSON-based web interfaces for command-line programs
avilella/RDE-PPI
:mountain: Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction (ICLR 2023)
avilella/RoseTTAFold2
avilella/SPACE2
Tool for rapid clustering of antibody models by the structure of their CDRs.
avilella/sword
tool for finding similar word in a file
avilella/Uni-Fold
An open-source platform for developing protein models beyond AlphaFold.
avilella/wgbs_tools
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies