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Search results for python genomics

372 search results found

Pandas Genomics ⭐ 42

Pandas ExtensionDtypes for dealing with genomics data

ClairS - a deep-learning method for long-read somatic small variant calling

Pymsaviz ⭐ 41

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

Balsamic ⭐ 40

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Jgi Query ⭐ 40

A simple command-line tool to download data from Joint Genome Institute databases

Biopython Coronavirus ⭐ 39

Biopython Jupyter Notebook tutorial to characterize a small genome

Automated Modelling for Biological Evidence-based Research

Aniclustermap ⭐ 38

A tool for drawing ANI clustermap between all-vs-all microbial genomes

de novo virus assembler of Illumina paired reads

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

Hicpeaks ⭐ 36

A Python implementation for BH-FDR and HiCCUPS

An opinionated Cromwell orchestration manager.

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

Biocommons.seqrepo ⭐ 34

non-redundant, compressed, journalled, file-based storage for biological sequences

Mandrake ⭐ 34

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Read specialized NGS formats as data frames in R, Python, and more.

Genome-wide reconstruction of complex structural variants

Makeflow Examples ⭐ 31

Example workflows for the Makeflow workflow system.

lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

Toil Scripts ⭐ 30

Toil workflows for common genomic pipelines

Interactive software tool for the assignment of cell types in single-cell studies.

A python package and a set of shell commands to handle GTF files

Toil Rnaseq ⭐ 29

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

Minimum Information about any (X) Sequence” (MIxS) specification

Stratipy ⭐ 29

Graph regularized nonnegative matrix factorization (GNMF) in Python

The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline

Ready-to-go Parquet-formatted public 'omics datasets

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Ezancestry ⭐ 28

Easy genetic ancestry predictions in Python

Some useful python scripts for biologists

Cogclassifier ⭐ 27

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

A tool for fast and accurate summarizing of variant calling format (VCF) files

Busco_phylogenomics ⭐ 26

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

Varsome Api Client Python ⭐ 26

Example client programs for Saphetor's VarSome annotation API

Genome-wide imputation pipeline

Create WDL documentation using Markdown.

Smallrnaseq ⭐ 26

small rna-seq analysis package

Genomics Operations ⭐ 26

A public reference implementation of HL7 FHIR Genomics Operations (http://build.fhir.org/ig/HL7/genomics-reporting/o

skDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

Environmental DNA metabarcoding taxonomic identification

Teaching ⭐ 25

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

Forward-time simulation in Python using fwdpp

Tandem repeat expansion detection or genotyping from long-read alignments

Gdctools ⭐ 24

Python and UNIX CLI utilities to simplify interaction with the NIH/NCI Genomics Data Commons

Chromoformer ⭐ 24

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

Python bindings to UCSC BigWig and BigBed library

Genomics database manager

mapping pipeline for ancient DNA

Python library and scripts for retrieval and storage of genomics data in HDF5 format

Openomics ⭐ 23

A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.

Go_enrichment ⭐ 23

Transcripts annotation and GO enrichment Fisher tests

Nmdc Schema ⭐ 23

This repository contains the LinkML specification for the NMDC schema and the artifacts generated by LinkML.

Phylociraptor ⭐ 23

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Discover ⭐ 23

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Pgltools ⭐ 23

Paired Genomic Loci Tool Suite

Order and orientation of complete bacterial genomes

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

Sequencework ⭐ 22

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters

UniProt Id Mapping through API

Cmdbtools ⭐ 21

Command line tools for CMDB varaints browser

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

a versatile toolkit for processing and analyzing diverse types of sequence data

Vcf2fhir ⭐ 20

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration

A toolkit for prokaryotic comparative genomics

Predict plasmids from uncorrected long read data

Mgcplotter ⭐ 20

Microbial Genome Circular plotting tool for comparative genomics using Circos

Gff3toembl ⭐ 20

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Sgidspace ⭐ 19

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Complex structural variant detection from WGS data

Metagenomic Deepfri ⭐ 19

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Hts Python ⭐ 18

pythonic wrapper for htslib

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Clairs To ⭐ 18

ClairS-TO - a deep-learning method for tumor-only somatic SNV calling

Cgl Docker Lib ⭐ 18

Smcounter ⭐ 18

smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller", BMC Genomics, 2017 18:5. https://bmcgenomics.biomedcentral.com/articles/10.

Tool to estimate deltas for sequence sets and answer questions about relative contribution

Genomic Features ⭐ 17

Genomic Features in Python from BioConductor's AnnotationHub

Manage the visualization of large amounts of other people's [often messy] genomics data

Python wrapper for wavefront alignment using WFA2-lib

Find target sites for the miRNAs in genomic sequences

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

Centroflye ⭐ 17

An algorithm for centromere assembly using long error-prone reads

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

PyPop: Python for Population Genomics

Tredparse ⭐ 17

TREDPARSE: HLI Short Tandem Repeat (STR) caller

⛓️ Construct a Physical Map from Linked Reads

GenoML (genoml2) is an open source Python package. It is an automated machine learning (autoML) platform for genomics data

Quality of life improvements for Bioinformatics in Python.

A tool to extract LOH blocks from VCF, BAM and FASTA data

Tools for producing pseudo-cgh of next-generation sequencing data

Make_lastz_chains ⭐ 17

Portable solution to generate genome alignment chains using lastz

10x_snakepipe ⭐ 17

A snakemake pipeline for 10X genomics cellranger

A package for designing activity-informed nucleic acid diagnostics for viruses.

A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.

A Framework to call Structural Variants from NGS based datasets

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