avalind

Anders Valind's starred repositories

patterns

A curated collection of Nextflow implementation patterns

Language:NextflowMIT33100

containerize-conda

Turn an existing conda environment into a Singularity container

Language:Python7800

conda-lock

Lightweight lockfile for conda environments

Language:PythonNOASSERTION49200

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:PythonMIT3700

sccomp

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

Language:R9300

simdeez

easy simd

Language:RustMIT33500

gggenomes

A grammar of graphics for comparative genomics

Language:RNOASSERTION59300

faceswap

Deepfakes Software For All

Language:PythonGPL-3.05225900

open-pedigree

A free and open-source pedigree tool by PhenoTips®

Language:JavaScriptLGPL-2.14600

ClinSV

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

Language:PerlNOASSERTION6500

TerminalExtensions.jl

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

Language:JuliaNOASSERTION4200

AGAT

Another Gtf/Gff Analysis Toolkit

Language:PerlGPL-3.045500

rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

Language:JavaBSD-2-Clause29500

phaser

phasing and Allele Specific Expression from RNA-seq

Language:PythonGPL-3.010900

arcasHLA-quant

Language:PythonGPL-3.0600

QDNAseq.hg38

QDNAseq bin annotation for hg38

Language:RGPL-3.01500

pajp

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

Language:Python200

valr

Genome Interval Arithmetic in R

Language:RNOASSERTION8800

ctree

Clone trees for Cancer Evolution studies from bulk sequencing data.

Language:R500

getzlab-LNP

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

Language:MATLAB500

ideogram

Chromosome visualization for the web

Language:JavaScriptNOASSERTION29300

truvari

Structural variant toolkit for VCFs

Language:PythonMIT32100

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:RoffBSD-3-Clause6800