Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

pypi.org "sequencing" keyword

snpmatch 4.0.0
A simple python library to identify the most likely strain given the SNPs for a sample
14 versions - Latest release: over 4 years ago - 1 dependent repositories - 123 downloads last month - 9 stars on GitHub - 2 maintainers
ngsphy 1.0.13
phylogenomic simulation of NGS data
13 versions - Latest release: about 6 years ago - 1 dependent repositories - 117 downloads last month - 14 stars on GitHub - 2 maintainers
vatools 5.1.1
A tool for annotating VCF files with expression and readcount data
9 versions - Latest release: 3 months ago - 1 dependent repositories - 233 downloads last month - 24 stars on GitHub - 6 maintainers
divvy 0.6.0
A python-based configuration manager for portable environment configurations
12 versions - Latest release: over 2 years ago - 1 dependent package - 5 dependent repositories - 302 downloads last month - 4 stars on GitHub - 8 maintainers
Top 9.9% on pypi.org
pvactools 4.1.1
A cancer immunotherapy tools suite
74 versions - Latest release: about 2 months ago - 1 dependent repositories - 635 downloads last month - 125 stars on GitHub - 3 maintainers
readfish 2024.2.0
ONT adaptive sampling
10 versions - Latest release: 3 days ago - 1 dependent repositories - 285 downloads last month - 161 stars on GitHub - 6 maintainers
Top 3.0% on pypi.org
hgvs 1.5.4
HGVS Parser, Formatter, Mapper, Validator
73 versions - Latest release: over 1 year ago - 5 dependent packages - 34 dependent repositories - 37.5 thousand downloads last month - 231 stars on GitHub - 2 maintainers
Top 4.6% on pypi.org
biocommons.seqrepo 0.6.9
Non-redundant, compressed, journalled, file-based storage for biological sequences
45 versions - Latest release: 3 months ago - 8 dependent packages - 21 dependent repositories - 63.8 thousand downloads last month - 38 stars on GitHub - 4 maintainers
Top 5.6% on pypi.org
bioutils 0.5.8
miscellaneous simple bioinformatics utilities and lookup tables
59 versions - Latest release: 10 months ago - 6 dependent packages - 28 dependent repositories - 84.8 thousand downloads last month - 17 stars on GitHub - 4 maintainers
Top 9.9% on pypi.org
iva 1.0.9
Iterative Virus Assembler
16 versions - Latest release: over 6 years ago - 5 dependent repositories - 87 downloads last month - 52 stars on GitHub - 2 maintainers
starseqr 0.6.7
RNA-Fusion Calling with STAR
24 versions - Latest release: about 6 years ago - 1 dependent repositories - 85 downloads last month - 15 stars on GitHub - 1 maintainer
looper 1.7.0
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
18 versions - Latest release: 4 months ago - 5 dependent repositories - 332 downloads last month - 19 stars on GitHub - 6 maintainers
pipestat 0.9.1
A pipeline results reporter
36 versions - Latest release: 18 days ago - 3 dependent packages - 3 dependent repositories - 18.1 thousand downloads last month - 4 stars on GitHub - 2 maintainers
Top 9.3% on pypi.org
sequenza-utils 3.0.0
Analysis of cancer sequencing samples, utilities for the sequenza R package
2 versions - Latest release: about 5 years ago - 2 dependent repositories - 405 downloads last month - 2 maintainers
seqm 0.1.0
Utilities for calculating sequence metrics.
4 versions - Latest release: about 3 years ago - 1 dependent repositories - 51 downloads last month - 0 stars on GitHub - 2 maintainers
yapyseq 1.1.0
Yet Another Python Sequencer
2 versions - Latest release: almost 5 years ago - 1 dependent repositories - 18 downloads last month - 1 stars on GitHub - 2 maintainers
cemba-data 1.6.9
Pipelines for single nucleus methylome and multi-omic dataset.
55 versions - Latest release: 12 months ago - 1 dependent repositories - 151 downloads last month - 14 stars on GitHub - 2 maintainers
ngcgh 0.4.4
Pseudo-cgh of next-generation sequencing data
15 versions - Latest release: over 10 years ago - 1 dependent repositories - 64 downloads last month - 17 stars on GitHub - 2 maintainers
pararead 0.7.0
Parallel processing of sequencing reads
4 versions - Latest release: over 4 years ago - 1 dependent package - 3 dependent repositories - 117 downloads last month - 8 stars on GitHub - 8 maintainers
pvacseq 4.0.10
Personalized Variant Antigens by Cancer Sequencing (pVAC-Seq)
20 versions - Latest release: over 6 years ago - 2 dependent repositories - 80 downloads last month - 60 stars on GitHub - 4 maintainers
boss_runs 0.1.0
Dynamic, adaptive sampling during nanopore sequencing
1 version - Latest release: 2 months ago - 27 downloads last month - 161 stars on GitHub - 2 maintainers
deepac 0.14.1
Predicting pathogenic potentials of novel DNA with reverse-complement neural networks.
19 versions - Latest release: over 1 year ago - 8 dependent repositories - 211 downloads last month - 2 stars on GitLab.com - 2 maintainers
Top 2.0% on pypi.org
multiqc 1.10.1
Create aggregate bioinformatics analysis reports across many samples and tools
34 versions - Latest release: about 3 years ago - 2 dependent packages - 74 dependent repositories - 8.78 thousand downloads last month - 1,162 stars on GitHub - 1 maintainer
bookend-rna 1.2.1
End-guided transcript assembler for short and long RNA-seq reads.
17 versions - Latest release: 8 months ago - 1 dependent repositories - 59 downloads last month - 13 stars on GitHub - 1 maintainer
Top 8.5% on pypi.org
truvari 4.2.2
Structural variant comparison tool for VCFs
26 versions - Latest release: about 1 month ago - 2 dependent repositories - 711 downloads last month - 291 stars on GitHub - 1 maintainer
mbin 1.1.1
mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
3 versions - Latest release: about 6 years ago - 1 dependent repositories - 23 downloads last month - 25 stars on GitHub - 2 maintainers
Top 3.1% on pypi.org
airr 1.5.0
AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data.
7 versions - Latest release: 8 months ago - 7 dependent packages - 11 dependent repositories - 3.25 thousand downloads last month - 34 stars on GitHub - 6 maintainers
markmeld 0.3.0
Markmeld is a markup melder that combines structured yaml or markdown data into templated markdow...
4 versions - Latest release: 6 months ago - 1 dependent repositories - 32 downloads last month - 3 maintainers
pyseq2500 0.64
Control an Illumina HiSeq 2500 System
8 versions - Latest release: about 2 years ago - 1 dependent repositories - 56 downloads last month - 18 stars on GitHub - 2 maintainers
ont-tombo 1.5.1
Analysis of raw nanopore sequencing data.
12 versions - Latest release: about 4 years ago - 1 dependent repositories - 145 downloads last month - 220 stars on GitHub - 2 maintainers
Top 4.3% on pypi.org
nf-core 2.14.1
Helper tools for use with nf-core Nextflow pipelines.
48 versions - Latest release: 3 days ago - 1 dependent package - 4 dependent repositories - 9.17 thousand downloads last month - 216 stars on GitHub - 4 maintainers
yanagiba 1.0.0
Filter short or low quality Oxford Nanopore reads which have been basecalled with Albacore.
2 versions - Latest release: over 6 years ago - 1 dependent repositories - 17 downloads last month - 1 stars on GitHub - 2 maintainers
galaxy-test-api 24.0.2
Galaxy API tests
18 versions - Latest release: 5 days ago - 1 dependent repositories - 186 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-tours 24.0.2
Galaxy tours backend framework
15 versions - Latest release: 5 days ago - 1 dependent package - 362 downloads last month - 1,315 stars on GitHub - 2 maintainers
Top 5.1% on pypi.org
galaxy-web-stack 24.0.2
Galaxy web stack abstraction
18 versions - Latest release: 5 days ago - 3 dependent packages - 10 dependent repositories - 437 downloads last month - 1,315 stars on GitHub - 6 maintainers
Top 5.1% on pypi.org
galaxy-web-framework 24.0.2
Galaxy web framework
19 versions - Latest release: 5 days ago - 4 dependent packages - 10 dependent repositories - 423 downloads last month - 1,315 stars on GitHub - 6 maintainers
Top 4.9% on pypi.org
galaxy-data 24.0.2
Galaxy datatype framework and datatypes
24 versions - Latest release: 5 days ago - 8 dependent packages - 13 dependent repositories - 782 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-selenium 24.0.2
Galaxy Selenium interaction framework
19 versions - Latest release: 5 days ago - 1 dependent repositories - 222 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-web-apps 24.0.2
Galaxy web apps
15 versions - Latest release: 5 days ago - 1 dependent package - 1 dependent repositories - 233 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.1% on pypi.org
galaxy-job-execution 24.0.2
Galaxy job execution runtime utilities
20 versions - Latest release: 5 days ago - 5 dependent packages - 10 dependent repositories - 430 downloads last month - 1,315 stars on GitHub - 6 maintainers
Top 3.6% on pypi.org
galaxy-objectstore 24.0.2
Galaxy objectstore framework and plugins
25 versions - Latest release: 5 days ago - 5 dependent packages - 13 dependent repositories - 824 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 3.8% on pypi.org
galaxy-job-metrics 24.0.2
Galaxy job metrics
22 versions - Latest release: 5 days ago - 3 dependent packages - 10 dependent repositories - 665 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 5.4% on pypi.org
galaxy-files 24.0.2
Galaxy file source framework and default plugins
16 versions - Latest release: 5 days ago - 4 dependent packages - 6 dependent repositories - 499 downloads last month - 1,315 stars on GitHub - 6 maintainers
Top 6.1% on pypi.org
galaxy-config 24.0.2
Galaxy configuration
16 versions - Latest release: 5 days ago - 3 dependent packages - 3 dependent repositories - 393 downloads last month - 1,315 stars on GitHub - 5 maintainers
Top 5.2% on pypi.org
galaxy-auth 24.0.2
Galaxy auth framework and implementations
19 versions - Latest release: 5 days ago - 2 dependent packages - 10 dependent repositories - 396 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 6.1% on pypi.org
galaxy-test-base 24.0.2
Galaxy testing utilities
18 versions - Latest release: 5 days ago - 2 dependent packages - 9 dependent repositories - 272 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-test-driver 24.0.2
Galaxy test driver
18 versions - Latest release: 5 days ago - 1 dependent package - 1 dependent repositories - 185 downloads last month - 1,315 stars on GitHub - 6 maintainers
galaxy-navigation 24.0.2
Galaxy client DOM navigation framework
15 versions - Latest release: 5 days ago - 2 dependent packages - 417 downloads last month - 1,315 stars on GitHub - 2 maintainers
Top 1.6% on pypi.org
galaxy-tool-util 24.0.2
Galaxy tool and tool dependency utilities
60 versions - Latest release: 5 days ago - 15 dependent packages - 43 dependent repositories - 17.9 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 1.9% on pypi.org
galaxy-util 24.0.2
Galaxy generic utilities
36 versions - Latest release: 5 days ago - 21 dependent packages - 23 dependent repositories - 16.7 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-tool-shed 24.0.2
Galaxy auth framework and implementations
4 versions - Latest release: 5 days ago - 102 downloads last month - 1,315 stars on GitHub - 2 maintainers
galaxy-schema 24.0.2
Galaxy auth framework and implementations
4 versions - Latest release: 5 days ago - 111 downloads last month - 1,315 stars on GitHub - 2 maintainers
Top 4.4% on pypi.org
galaxy-app 24.0.2
Galaxy application (backend)
19 versions - Latest release: 5 days ago - 4 dependent packages - 13 dependent repositories - 450 downloads last month - 1,315 stars on GitHub - 3 maintainers
savemoney 0.2.16
Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You!
13 versions - Latest release: about 2 months ago - 194 downloads last month - 9 stars on GitHub - 2 maintainers
seroba 1.0.0
SEROBA: Serotyping for illumina reads
3 versions - Latest release: over 6 years ago - 1 dependent repositories - 11 downloads last month - 15 stars on GitHub - 2 maintainers
varvamp 1.1.3
Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses
21 versions - Latest release: 16 days ago - 217 downloads last month - 17 stars on GitHub - 1 maintainer
relecov-tools 0.0.5
Tools for managing and resolution of buisciii services.
3 versions - Latest release: over 1 year ago - 2 dependent repositories - 25 downloads last month - 4 stars on GitHub - 2 maintainers
Top 6.9% on pypi.org
nanoplot 1.42.0
Plotting suite for Oxford Nanopore sequencing data and alignments
151 versions - Latest release: 7 months ago - 3 dependent repositories - 1.3 thousand downloads last month - 388 stars on GitHub - 1 maintainer
seqpipe 0.0.7
Sequencing pipeline
5 versions - Latest release: over 6 years ago - 1 dependent repositories - 8 downloads last month - 1 stars on GitHub - 2 maintainers
filter_variants 0.2.1
Filter variants based on frequencies
4 versions - Latest release: over 8 years ago - 2 dependent repositories - 28 downloads last month - 0 stars on GitHub - 2 maintainers
mirror_seq 0.2.6
The bioinformatics tool for Mirror-seq.
8 versions - Latest release: almost 8 years ago - 2 dependent repositories - 37 downloads last month - 1 stars on GitHub - 2 maintainers
bioa 1.24
Library for viral diversity estimation and identification using next-gen sequencing data.
2 versions - Latest release: almost 11 years ago - 2 dependent repositories - 38 downloads last month - 2 maintainers
Top 6.8% on pypi.org
pyfastaq 3.17.0
Script to manipulate FASTA and FASTQ files, plus API for developers
21 versions - Latest release: about 6 years ago - 42 dependent repositories - 646 downloads last month - 68 stars on GitHub - 2 maintainers
deepsvr 0.0.1.post1
Automated Somatic Variant Refinement by Deep Learning
1 version - Latest release: about 6 years ago - 1 dependent repositories - 11 downloads last month - 49 stars on GitHub - 2 maintainers
Top 3.5% on pypi.org
refgenie 0.12.1
Refgenie creates a standardized folder structure for reference genome files and indexes. You can ...
25 versions - Latest release: over 2 years ago - 1 dependent package - 10 dependent repositories - 5.97 thousand downloads last month - 67 stars on GitHub - 4 maintainers
Top 2.2% on pypi.org
refgenconf 0.12.2
A standardized configuration object for reference genome assemblies
27 versions - Latest release: over 2 years ago - 2 dependent packages - 40 dependent repositories - 33 thousand downloads last month - 3 stars on GitHub - 4 maintainers
Top 5.5% on pypi.org
changeo 1.3.0
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
25 versions - Latest release: over 1 year ago - 1 dependent package - 7 dependent repositories - 689 downloads last month - 5 maintainers
nanosplit 0.1.4
Perform splitting of Oxford Nanopore sequencing data in a fail and pass dataset.
5 versions - Latest release: almost 7 years ago - 1 dependent repositories - 22 downloads last month - 1 stars on GitHub - 2 maintainers
murphy 0.1
Generic tools to identify overlapping genomic regions
1 version - Latest release: almost 7 years ago - 1 dependent repositories - 8 downloads last month - 0 stars on GitHub - 2 maintainers
geniml 0.3.0
Genomic interval toolkit
3 versions - Latest release: about 1 month ago - 388 downloads last month - 4 maintainers
Top 6.6% on pypi.org
chanjo 4.6.1
Coverage analysis tool for clinical sequencing
62 versions - Latest release: over 2 years ago - 2 dependent packages - 4 dependent repositories - 1.03 thousand downloads last month - 6 maintainers
chanjo-ccds 0.1
CCDS to Chanjo BED converter
4 versions - Latest release: 9 months ago - 2 dependent repositories - 23 downloads last month - 1 maintainer
ssub 0.2.1
Polls a GCP Pub/Sub topic for new SampleSheet notification messages in order to initiate bcl2fastq.
3 versions - Latest release: about 4 years ago - 1 dependent repositories - 33 downloads last month - 2 maintainers
fings 1.7.1
Filters for Next Generation Sequencing
4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 46 downloads last month - 8 stars on GitHub - 2 maintainers
wormbase-parasite 0.5.0
An interface to the Wormbase REST API
3 versions - Latest release: about 3 years ago - 1 dependent repositories - 46 downloads last month - 3 stars on GitHub - 1 maintainer
kman 0.0.1
K-mer management tools
1 version - Latest release: about 6 years ago - 1 dependent repositories - 4 downloads last month - 0 stars on GitHub - 2 maintainers
bioutil 0.4.0
Bioinfomatics File access tools
5 versions - Latest release: over 5 years ago - 43 downloads last month - 1 stars on GitHub - 2 maintainers
simulatesv 0.2.0
Simulate structural variations and SNPs with artificial dna sequences
4 versions - Latest release: almost 7 years ago - 1 dependent repositories - 12 downloads last month - 1 stars on GitHub - 1 maintainer
cosmos-wfm 2.13.11
Workflow Management System
229 versions - Latest release: over 3 years ago - 4 dependent repositories - 481 downloads last month - 70 stars on GitHub - 2 maintainers
hmobster 0.0.44
VAF clustering for multiple karyotypes
40 versions - Latest release: over 1 year ago - 1 dependent repositories - 321 downloads last month - 1 stars on GitHub - 2 maintainers
ngstk 0.0.1rc2
Next-generation sequencing utility functions
3 versions - Latest release: almost 5 years ago - 1 dependent repositories - 29 downloads last month - 1 stars on GitHub - 4 maintainers
seq-pigeon 0.4.3
Pipeline tool for NGS data
17 versions - Latest release: over 3 years ago - 1 dependent repositories - 89 downloads last month - 933 stars on GitHub - 2 maintainers
nanorepeat 1.4.1
NanoRepeat: quantification of Short Tandem Repeats (STRs) from long-read sequencing data
6 versions - Latest release: 12 months ago - 45 downloads last month - 15 stars on GitHub - 2 maintainers
de-toolkit 0.9.12
Suite of tools for working with count data
29 versions - Latest release: over 4 years ago - 1 dependent repositories - 169 downloads last month - 2 maintainers
barcode-splitter 0.18.6
A utility to split multiple sequence files using multiple sets of barcodes
7 versions - Latest release: almost 5 years ago - 70 downloads last month - 4 maintainers
gisaid-download 0.3.0
Assisted download of selected gisaid metadata or EPI_SET creation
2 versions - Latest release: about 1 year ago - 17 downloads last month - 0 stars on GitHub - 2 maintainers
reviewer2 0.9.31
Starts a simple image server that lets you quickly flip through image files from a local director...
24 versions - Latest release: almost 3 years ago - 1 dependent repositories - 127 downloads last month - 18 stars on GitHub - 2 maintainers
s-rna-tools 0.0.3
Tools for handling Small RNA sequences.
3 versions - Latest release: over 1 year ago - 11 downloads last month - 0 stars on GitHub - 2 maintainers
pvacseq-client 0.0.2
Web Front-End for pVAC-Seq
3 versions - Latest release: about 7 years ago - 1 dependent package - 1 dependent repositories - 16 downloads last month - 0 stars on GitHub - 6 maintainers
pyfq 0.0.6
Fastq manipulations and quality check
6 versions - Latest release: over 5 years ago - 1 dependent repositories - 49 downloads last month - 2 maintainers
flipbook 1.0.1
Starts a simple image server that lets you quickly flip through image files from a local director...
18 versions - Latest release: 4 months ago - 1 dependent repositories - 76 downloads last month - 18 stars on GitHub - 1 maintainer
diva-seq-opt 0.0.3
Predict the library loading concentration to use for mi-seq runs based on bioanalyzer data.
3 versions - Latest release: about 5 years ago - 1 dependent repositories - 17 downloads last month - 1 stars on GitHub - 2 maintainers
pacbiodataprocessing 1.3.0
Tools to process PacBio sequencing data at molecule level
24 versions - Latest release: over 1 year ago - 1 dependent repositories - 135 downloads last month - 0 stars on GitLab.com - 2 maintainers
genetables 0.1.1
Genome table processing
4 versions - Latest release: almost 8 years ago - 2 dependent repositories - 18 downloads last month - 2 maintainers
sruns-monitor 1.2.0
Looks for new Illumina sequencing runs and tars them up into GCP storage
19 versions - Latest release: about 4 years ago - 1 dependent repositories - 151 downloads last month - 2 maintainers
omicidx-builder 0.5.1
Tooling to build and deploy omicidx data and resources
9 versions - Latest release: almost 4 years ago - 1 dependent repositories - 87 downloads last month - 3 stars on GitHub - 2 maintainers
geo-upload-tool 1.0.8
CLI tool for preparing data submission to Gene Expression Omnibus
9 versions - Latest release: almost 3 years ago - 1 dependent repositories - 65 downloads last month - 2 maintainers
fdstools 2.0.4
Forensic DNA Sequencing Tools
13 versions - Latest release: about 1 year ago - 2 dependent repositories - 363 downloads last month - 5 stars on GitHub - 1 maintainer
snoopy 0.4.7
Browser based quality control tool to expedite reviewing predicted variants in next generation se...
7 versions - Latest release: over 7 years ago - 3 dependent repositories - 58 downloads last month - 9 stars on GitHub - 2 maintainers
ediacara 0.2.2
EGF's alignment reporter
2 versions - Latest release: 9 months ago - 16 downloads last month - 1 maintainer
Related Keywords
bioinformatics 113 genomics 65 ngs 53 workflow 39 pipeline 35 dna 33 science 30 hacktoberfest 28 usegalaxy 26 workflow-engine 26 biology 25 Galaxy 21 NGS 20 nanopore 19 python 12 DNA 12 variant 11 project 10 next generation sequencing 9 quality 9 control 8 cancer 8 metadata 8 genome 8 plotting 7 next-generation-sequencing 7 variants 7 bioinformatics-pipeline 7 rna-seq 7 quality control 7 learning 6 deep 6 genome-analysis 6 global-health 6 infectious-diseases 6 pathogen 6 research 6 processing 6 analysis 6 prediction 5 variation 5 variant-analysis 5 genetics 5 galaxy 5 next 5 RNA-seq 5 generation 5 clinical 4 rna 4 sequence 4 exome 4 illumina 4 GUI 4 adaptive immunity 4 immunoglobulin 4 pathogenicity 4 quality-control 4 synthetic 4 oxford-nanopore 4 algorithmic-composition 4 reporting 4 music 4 midi 4 VCF 4 composition 4 methylation 3 python3 3 bioconda 3 data-visualization 3 multiqc 3 pypi 3 seqera 3 vizualisation 3 notation 3 generative-art 3 csound 3 creative-coding 3 high-throughput 3 alignment 3 immunology 3 AIRR-seq 3 adaptive immune receptor repertoires 3 filtering 3 coverage 3 fusion 3 neoantigens 3 antigens 3 pipeline-submission-engine 3 expression 3 assembly 3 molecular-biology 3 allele 3 VAF 3 B cell repertoire analysis 2 REviewer 2 read visualization 2 fasta 2 bed 2 deep learning 2 human 2