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The Top 23 Python Genomics Open Source Projects

Open source projects categorized as Python Genomics
Categories > Science > Genomics
Pandas Genomics ⭐ 42
Pandas ExtensionDtypes for dealing with genomics data
dependent packages 1total releases 21most recent commit a year agopypi pandas-genomics} Downloads
Clairs ⭐ 42
ClairS - a deep-learning method for long-read somatic small variant calling
most recent commit 3 months ago
Pymsaviz ⭐ 41
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
total releases 6most recent commit 7 months ago
Balsamic ⭐ 40
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
most recent commit 3 months ago
Jgi Query ⭐ 40
A simple command-line tool to download data from Joint Genome Institute databases
most recent commit 2 years ago
Biopython Coronavirus ⭐ 39
Biopython Jupyter Notebook tutorial to characterize a small genome
most recent commit 4 years ago
Amber ⭐ 39
Automated Modelling for Biological Evidence-based Research
most recent commit a year ago
Aniclustermap ⭐ 38
A tool for drawing ANI clustermap between all-vs-all microbial genomes
total releases 5most recent commit 5 months ago
Iva ⭐ 37
de novo virus assembler of Illumina paired reads
total releases 16most recent commit 3 years ago
Gor ⭐ 37
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.
most recent commit 4 months ago
Hicpeaks ⭐ 36
A Python implementation for BH-FDR and HiCCUPS
total releases 14most recent commit 8 months ago
Oliver ⭐ 36
An opinionated Cromwell orchestration manager.
total releases 27most recent commit a year ago
Advntr ⭐ 35
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
most recent commit 3 months ago
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Mandrake ⭐ 34
Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
total releases 2most recent commit 4 months ago
Oxbow ⭐ 32
Read specialized NGS formats as data frames in R, Python, and more.
dependent packages 2total releases 3most recent commit 4 months agopypi oxbow} Downloads
Grocsvs ⭐ 32
Genome-wide reconstruction of complex structural variants
most recent commit 4 years ago
Makeflow Examples ⭐ 31
Example workflows for the Makeflow workflow system.
most recent commit 10 months ago
Lsabgc ⭐ 31
lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters
total releases 10most recent commit 3 months ago
Wochenende ⭐ 30
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
most recent commit 2 years ago
Toil Scripts ⭐ 30
Toil workflows for common genomic pipelines
total releases 173most recent commit 5 years ago
Cellar ⭐ 30
Interactive software tool for the assignment of cell types in single-cell studies.
most recent commit a year ago
Pygtftk ⭐ 30
A python package and a set of shell commands to handle GTF files
total releases 29most recent commit a year ago
The 10 Latest Releases In Python Genomics Open Source Projects
Soda ⭐ 12
Python-based UCSC genome browser snapshot-taker and gallery-maker
total releases 2latest release June 14, 2021most recent commit 3 years ago
Mimsi ⭐ 12
Microsatellite Instability Classification using Multiple Instance Learning
total releases 1latest release March 26, 2021most recent commit 2 years ago
Genipe ⭐ 26
Genome-wide imputation pipeline
total releases 13latest release February 11, 2021most recent commit 3 years ago
Poppunk ⭐ 71
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
total releases 22latest release December 31, 2020most recent commit 4 months ago
Smallrnaseq ⭐ 26
small rna-seq analysis package
total releases 6latest release October 23, 2020most recent commit a year ago
Epivizfileserver ⭐ 5
Python library to query and transform genomic data from indexed files
total releases 30latest release October 16, 2020most recent commit 2 years ago
Gcgc ⭐ 8
An ML-feature processing library for biological sequences.
total releases 67latest release October 14, 2020most recent commit 4 years ago
Genotype ⭐ 7
Simple genotype comparison of VCF files
dependent packages 1total releases 9latest release September 23, 2020most recent commit a year agopypi genotype} Downloads
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