tzhang-nmdp Goto Github PK

2021-snakemake-checkpoints-example

agc

Assembled Genomes Compressor

alphafold

Open source code for AlphaFold.

alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

annotsv

Annotation and Ranking of Structural Variation

atac-seq-pipeline

ENCODE ATAC-seq pipeline

autoencoders-variants

Pytorch implementations of various types of autoencoders

awesome-gans

Awesome Generative Adversarial Networks with tensorflow

awesome-pangenomes

A list of software for pangenomics

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

bridgmodel2graph

BRIDG Model by version used to populate a Graph Database.

canu

A single molecule sequence assembler for genomes large and small.

captum

Model interpretability and understanding for PyTorch

ccpower

SAS macro for sample size/power calculation for case-cohort studies

cellrangerrkit

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

chip_calling_pipeline

Pipeline to call CHIP from WGS CRAM files.

chromsyn

Chromosome-level synteny plotting using orthologous regions

cnapy

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

consensusclustering

Shiny application implementing Consensus Clustering for various clustering algorithms.

cookhla

An accurate and efficient HLA imputation method.

coursera-gan-specialization

Programming assignments and quizzes from all courses within the GANs specialization offered by deeplearning.ai

ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19

cue

Deep learning framework for SV calling and genotyping

cyto-sv-ml

dash13-kir-mhc-assemblies

Repository for code and small data set for Dash13 Hackathon

dcen_chil2021

Implementation for RNA Alternative Splicing Prediction with Discrete Compositional Energy Network (ACM CHIL 2021)

deepcat

Deep Learning Method to Identify Cancer Associated TCRs