Awesome Open Source
Search
Programming Languages
Languages
All Categories
Categories
About
Search results for genomics
genomics
x
1,117 search results found
Biopython
⭐
3,918
Official git repository for Biopython (originally converted from CVS)
Deepvariant
⭐
2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Seurat
⭐
2,025
R toolkit for single cell genomics
Deeplearning Biology
⭐
1,846
A list of deep learning implementations in biology
Minimap2
⭐
1,613
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Gatk
⭐
1,576
Official code repository for GATK versions 4 and up
Bwa
⭐
1,282
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Pymatgen
⭐
1,254
Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.
Galaxy
⭐
1,211
Data intensive science for everyone.
Deep Review
⭐
1,186
A collaboratively written review paper on deep learning, genomics, and precision medicine
Vg
⭐
1,066
tools for working with genome variation graphs
Getting Started With Genomics Tools And Resources
⭐
991
Unix, R and python tools for genomics and data science
Adam
⭐
966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Hail
⭐
905
Cloud-native genomic dataframes and batch computing
Applied Computational Genomics
⭐
887
Applied Computational Genomics Course at UU: Spring 2020
Ncbi Genome Download
⭐
784
Scripts to download genomes from the NCBI FTP servers
Nucleus
⭐
675
Python and C++ code for reading and writing genomics data.
Goatools
⭐
673
Python library to handle Gene Ontology (GO) terms
Jcvi
⭐
650
Python library to facilitate genome assembly, annotation, and comparative genomics
Bwa Mem2
⭐
645
The next version of bwa-mem
Deeptools
⭐
644
Tools to process and analyze deep sequencing data.
Seq
⭐
624
A high-performance, Pythonic language for bioinformatics
Igv.js
⭐
608
Embeddable genomic visualization component based on the Integrative Genomics Viewer
Vcflib
⭐
603
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Bowtie2
⭐
594
A fast and sensitive gapped read aligner
Igv
⭐
589
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
Biojava
⭐
564
📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Orthofinder
⭐
547
Phylogenetic orthology inference for comparative genomics
Awesome Omics
⭐
536
A collection of awesome things regarding all omics.
Cbioportal
⭐
535
cBioPortal for Cancer Genomics
Eggnog Mapper
⭐
522
Fast genome-wide functional annotation through orthology assignment
Gggenomes
⭐
518
A grammar of graphics for comparative genomics
Scrna Seq_notes
⭐
478
A list of scRNA-seq analysis tools
Pycirclize
⭐
476
Circular visualization in Python (Circos Plot, Chord Diagram)
Hifiasm
⭐
443
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Megahit
⭐
442
Ultra-fast and memory-efficient (meta-)genome assembler
Jvarkit
⭐
440
Java utilities for Bioinformatics
Jbrowse
⭐
437
Full-featured and stable genome browser built with JavaScript and HTML5.
Pyfaidx
⭐
427
Efficient pythonic random access to fasta subsequences
Healthcare_ml
⭐
426
A curated list of ML|NLP resources for healthcare.
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Maftools
⭐
400
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Delly
⭐
397
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Hyena Dna
⭐
379
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
Pyranges
⭐
371
Performant Pythonic GenomicRanges
Minigraph
⭐
367
Proof-of-concept seq-to-graph mapper and graph generator
Enformer Pytorch
⭐
359
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Arvados
⭐
354
An open source platform for managing and analyzing biomedical big data
Genomicspapers
⭐
350
The Leek group guide to genomics papers
Cyvcf2
⭐
345
cython + htslib == fast VCF and BCF processing
Postgui
⭐
335
A React web application to query and share any PostgreSQL database.
Vcfanno
⭐
334
annotate a VCF with other VCFs/BEDs/tabixed files
Cellranger
⭐
314
10x Genomics Single Cell Analysis
Juicer
⭐
313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Dorado
⭐
309
Oxford Nanopore's Basecaller
Nucleotide Transformer
⭐
305
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Higlass
⭐
304
Fast, flexible and extensible genome browser.
Sarek
⭐
299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Dna Diffusion
⭐
297
🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
Awesome Bioinformatics Benchmarks
⭐
292
A curated list of bioinformatics bench-marking papers and resources.
Fgbio
⭐
292
Tools for working with genomic and high throughput sequencing data.
Octopus
⭐
285
Bayesian haplotype-based mutation calling
Truvari
⭐
284
Structural variant toolkit for VCFs
Hap.py
⭐
283
Haplotype VCF comparison tools
Canvasxpress
⭐
282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Genomeworks
⭐
276
SDK for GPU accelerated genome assembly and analysis
Htsjdk
⭐
271
A Java API for high-throughput sequencing data (HTS) formats.
Ideogram
⭐
265
Chromosome visualization for the web
Genometools
⭐
261
GenomeTools genome analysis system.
Rtg Tools
⭐
260
RTG Tools: Utilities for accurate VCF comparison and manipulation
Sequenceserver
⭐
259
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Bio.jl
⭐
256
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
Glow
⭐
251
An open-source toolkit for large-scale genomic analysis
Ribbon
⭐
251
A genome browser that shows long reads and complex variants better
Dragonn
⭐
245
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
Bedops
⭐
244
🔬 BEDOPS: high-performance genomic feature operations
Pygeno
⭐
242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Comp Genomics Class
⭐
236
Code and examples for JHU Computational Genomics class
Flowcraft
⭐
234
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
Intermine
⭐
228
A powerful open source data warehouse system
Hgvs
⭐
226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Vcfr
⭐
225
Tools to work with variant call format files
Somalier
⭐
224
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Kipoi
⭐
222
Kipoi's model zoo API
Slivar
⭐
221
genetic variant expressions, annotation, and filtering for great good.
Roary
⭐
219
Rapid large-scale prokaryote pan genome analysis
Dram
⭐
214
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Miso Lims
⭐
214
MISO: An open-source LIMS for NGS sequencing centres
Ga4gh Schemas
⭐
213
Models and APIs for Genomic data. RETIRED 2018-01-24
Giab_data_indexes
⭐
211
This repository contains data indexes from NIST's Genome in a Bottle project.
Janggu
⭐
205
Deep learning infrastructure for genomics
Amr
⭐
203
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Goleft
⭐
203
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Smudgeplot
⭐
200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Deep Rules
⭐
198
Ten Quick Tips for Deep Learning in Biology
Biomartr
⭐
198
Genomic Data Retrieval with R
Hicexplorer
⭐
197
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Miniasm
⭐
195
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Circlator
⭐
193
A tool to circularize genome assemblies
Clair3
⭐
191
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Related Searches
Bioinformatics Genomics (541)
Python Genomics (515)
Genome Genomics (297)
1-100 of 1,117 search results
Next >
Privacy
|
About
|
Terms
|
Follow Us On Twitter
Copyright 2018-2024 Awesome Open Source. All rights reserved.