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Sanity check Variant Call Format (VCF) files.

Python 37 24 Updated Mar 18, 2016

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.

Go 789 100 Updated Dec 27, 2024

A suite of tools for processing genotype data. Includes calling genotypes from .idat to plink (ped), sample/case-control variant QC steps, ancestry estimation. UNDER DEVELOPMENT

Python 14 3 Updated Dec 17, 2024

customizable pipeline to identify viral sequences from (meta)genomic data

Python 233 33 Updated Nov 28, 2024

A DSL for data-driven computational pipelines

Groovy 2,806 643 Updated Dec 23, 2024

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

C++ 796 264 Updated Jun 7, 2024

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

C++ 1,973 335 Updated Nov 28, 2024

SPAdes Genome Assembler

C++ 775 139 Updated Dec 25, 2024

Ultra-fast and memory-efficient (meta-)genome assembler

C++ 621 136 Updated Apr 30, 2024

Genome annotation with AUGUSTUS

C++ 291 111 Updated Nov 25, 2024
Jupyter Notebook 63 27 Updated Nov 21, 2024

Estimate recombination rates from population genetic data

C 61 20 Updated Jun 10, 2020

PHAST

C 70 24 Updated Dec 16, 2024

Haplotype based scans for selection

C 116 33 Updated Oct 22, 2024

Rare variant test software for next generation sequencing data

C++ 136 42 Updated Jan 26, 2022

deep residual neural network for classifying the pathogenicity of missense mutations.

Python 113 30 Updated Aug 25, 2021

Read-based phasing of genomic variants, also called haplotype assembly

Python 345 40 Updated Dec 20, 2024

phasing and Allele Specific Expression from RNA-seq

Python 110 35 Updated Jul 14, 2024

:atom: The hackable text editor

JavaScript 60,292 17,401 Updated Jan 3, 2023

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs a…

C 131 22 Updated Dec 4, 2024

Coding with all analyses performed in a project that aimed to study monkey proteins in a large number of genomes

1 Updated Mar 22, 2024

A python packaged version of RFMix (version 1)

C++ 6 1 Updated Sep 3, 2019

Calling local ancestry tracts with RFMix v1.5.4 and (optionally) validating global ancestry fractions with ADMIXTURE.

Python 3 2 Updated Mar 13, 2022

A protocol to estimate global ancestry starting from raw Illumina data

Python 10 4 Updated Oct 16, 2019

Documentation for the ANNOVAR software

235 366 Updated Oct 24, 2024

Download de dados do DataSUS e pré-processamento no R.

R 232 59 Updated Oct 31, 2024

A single molecule sequence assembler for genomes large and small.

C++ 664 179 Updated Dec 19, 2024

Tools for early stage alignment file processing

C++ 93 17 Updated Mar 12, 2019

Tools for bam file processing

C++ 55 20 Updated Apr 20, 2015

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

C++ 103 25 Updated Nov 14, 2024
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