avalind

avalind's Stars

• deepfakes/faceswap

  Deepfakes Software For All

  Language:Python52.8k1.5k86813.3k

• thackl/gggenomes

  A grammar of graphics for comparative genomics

  Language:R6321216165

• conda/conda-lock

  Lightweight lockfile for conda environments

  Language:Python50312294104

• NBISweden/AGAT

  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

  Language:Perl4764534457

• arduano/simdeez

  easy simd

  Language:Rust34093825

• nextflow-io/patterns

  A curated collection of Nextflow implementation patterns

  Language:Nextflow336252070

• ACEnglish/truvari

  Structural variant toolkit for VCFs

  Language:Python3331319149

• RealTimeGenomics/rtg-tools

  RTG Tools: Utilities for accurate VCF comparison and manipulation

  Language:Java30422048

• eweitz/ideogram

  Chromosome visualization for the web

  Language:JavaScript2942211671

• im3sanger/dndscv

  dN/dS methods to quantify selection in cancer and somatic evolution

  Language:HTML213139548

• 10XGenomics/vartrix

  Single-Cell Genotyping Tool

  Language:Rust201186326

• stephenturner/annotables

  R data package for annotating/converting Gene IDs

  Language:R162131833

• secastel/phaser

  phasing and Allele Specific Expression from RNA-seq

  Language:Python110107335

• MangiolaLaboratory/sccomp

  Testing differences in cell type proportions from single-cell data.

  Language:R948497

• rnabioco/valr

  Genome Interval Arithmetic in R

  Language:R89825325

• grst/containerize-conda

  Turn an existing conda environment into a Singularity container

  Language:Python795716

• raphael-group/hatchet

  HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

  Language:Roff691413832

• KCCG/ClinSV

  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

  Language:Perl6610698

• gerstung-lab/MutationTimeR

  An R package to time somatic mutations

  Language:R6041824

• phenotips/open-pedigree

  A free and open-source pedigree tool by PhenoTips®

  Language:JavaScript4691925

• Keno/TerminalExtensions.jl

  A package that makes Julia take advantage of cool terminal emulator features.

  Language:Julia4282411

• morrislab/pairtree

  Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.

  Language:Python3754211

• jason-weirather/hla-polysolver

  Fork of the Polysolver project

  Language:Perl3031518

• asntech/QDNAseq.hg38

  QDNAseq bin annotation for hg38

  Language:R14526

• roseorenbuch/arcasHLA-quant

  Language:Python6191

• broadinstitute/getzlab-LNP

  Log-normal-Poisson regression model from Hess et al. 2019

  Language:MATLAB5422

• caravagnalab/ctree

  Clone trees for Cancer Evolution studies from bulk sequencing data.

  Language:R5322

• avalind/pajp

  Somatic mutation calling on moderately deep WES data using GATK/MuTect

  Language:Python2100

• avalind/bloomlada

  C++ Implementation of a standard bloom filter, using MurmurHash (v2)

  Language:C++1101

• avalind/particles

  Me playing around with game physics.

  Language:JavaScript1100