#

genomics

Here are 1,787 public repositories matching this topic...

biopython / biopython

Open

Define SeqFeature sub for integer offset

2

peterjc commented Jan 1, 2022

See https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py and __add__, need to do the same specifically for integer offsets.

Workaround feature + (-5) instead of feature - 5, see https://twitter.com/tomeraltman/status/1473764959347638273

Read more

Enhancement good first issue

Open

silence warnings PDBConstructionWarning in test_PDB_StructureAlignment.py

4

Open

PAML run method docstrings - return value

16

Find more good first issues

google / deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

science machine-learning bioinformatics deep-learning genomics genome tensorflow ngs sequencing dna deep-neural-network deepvariant

Updated Jun 2, 2022
Python

broadinstitute / gatk

Official code repository for GATK versions 4 and up

java science bioinformatics spark genomics genome cluster ngs sequencing gatk-jar dna gatk

Updated Jun 3, 2022
Java

lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bioinformatics genomics sequence-alignment spliced-alignment

Updated May 14, 2022
C

greenelab / deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

review deep-learning genomics neural-networks manuscript manubot

Updated Dec 28, 2021
HTML

lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

bioinformatics genomics sequence-alignment fm-index

Updated May 19, 2022
C

galaxyproject / galaxy

Data intensive science for everyone.

docker science workflow bioinformatics pipeline genomics workflow-engine ngs sequencing dna usegalaxy hacktoberfest

Updated Jun 3, 2022
Python

bigdatagenomics / adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

python java bioinformatics r scala big-data spark avro genomics parquet

Updated May 23, 2022
Scala

vgteam / vg

tools for working with genome variation graphs

genomics graph dna variation-graph genome-graph

Updated Jun 2, 2022
C++

hail

hail-is / hail

Scalable genomic data analysis.

python bioinformatics gwas scala spark genomics genetics vcf software hail

Updated Jun 2, 2022
Python

google / nucleus

Python and C++ code for reading and writing genomics data.

bioinformatics genomics tensorflow dna

Updated Dec 9, 2021
C++

kblin / ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

python bioinformatics genomics command-line biology genbank ncbi-taxonomy ncbi refseq-genomes-belonging bacterial-refseq-genomes download-genomes fungal-genomes genbank-format mick-scripts older-versions

Updated Dec 1, 2021
Python

seq-lang / seq

A high-performance, Pythonic language for bioinformatics

python programming-language bioinformatics compiler genomics computational-biology domain-specific-language

Updated Dec 15, 2021
C++

bwa-mem2 / bwa-mem2

The next version of bwa-mem

bioinformatics genomics sequence-alignment

Updated Mar 31, 2022
C++

deeptools / deepTools

Tools to process and analyze deep sequencing data.

python bioinformatics rna-seq genomics ngs chip-seq

Updated May 18, 2022
Python

tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

bioinformatics genomics assembly blast comparative-genomics variant-calling synteny sequence-alignments genome-sequencing genetic-maps allmaps

Updated May 16, 2022
Python

tanghaibao / goatools

Python library to handle Gene Ontology (GO) terms

genomics gene-ontology bioinfomatics gene-set-enrichment sidak fdr goslim-terms fisher-tests fdr-benjamini holm-sidak

Updated Apr 3, 2022
Python

biojava / biojava

📖

🔬

☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

java bioinformatics genomics pdb parser-library protein-data-bank protein-structure protein-sequences sequence-alignment protein-modification structure-alignment structural-bioinformatics

Updated Apr 27, 2022
Java

vcflib / vcflib

C++ library and cmdline tools for parsing and manipulating VCF files

genomics variant-calling genotyping haplotypecaller vcf-manipulation

Updated Jun 1, 2022
C++

MareesAT / GWA_tutorial

A comprehensive tutorial about GWAS and PRS

unix bioinformatics gwas r genomics genetics plink prs population-structure qc population-stratification

Updated Jan 3, 2020

BenLangmead / bowtie2

A fast and sensitive gapped read aligner

c-plus-plus bioinformatics genomics read-aligners

Updated Apr 17, 2022
C++

GMOD / jbrowse

Open

alignments2 - change track height in track menu

6

keiranmraine commented Sep 28, 2016

Is this on anyone's radar? I know it's a simple item to add directly

Read more

feature req small task help wanted good first issue

Open

renumbering reference sequence for viral insertions

5

Open

add area graph of base quality behind alignment feature glyph

4

voutcn / megahit

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

bioinformatics genomics metagenomics data-structures succinct genome-assembly

Updated Apr 4, 2022
C++

jvarkit

lindenb / jvarkit

Java utilities for Bioinformatics

java science bioinformatics genomics wiki biology ngs java-utilities next-generation-sequencing

Updated Jun 1, 2022
Java

mdshw5 / pyfaidx

Efficient pythonic random access to fasta subsequences

python bioinformatics genomics indexing dna protein fasta samtools bgzf

Updated Jun 2, 2022
Python

eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

genomics annotations functional-annotation orthology-assignments

Updated Feb 17, 2022
Python

priyank-purohit / PostGUI

A React web application to query and share any PostgreSQL database.

Updated Jun 1, 2022
JavaScript

maftools

PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

bioinformatics r genomics tcga maf-files cancer-genomics cancer-genome-atlas

Updated May 20, 2022
R

arvados / arvados

An open source platform for managing and analyzing biomedical big data

ruby python go docker aws workflow cloud bioinformatics genomics azure workflow-engine cluster bigdata gcp cwl arvados

Updated Jun 2, 2022
Go

Illumina / hap.py

Haplotype VCF comparison tools

bioinformatics genomics vcf vcf-comparison

Updated Dec 13, 2021
C++

Improve this page

Add a description, image, and links to the genomics topic page so that developers can more easily learn about it.

Curate this topic

Add this topic to your repo

To associate your repository with the genomics topic, visit your repo's landing page and select "manage topics."