Ecosyste.ms: Packages

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

pypi.org "ngs" keyword

phageboost 0.1.7
a Fast Prophage and Phage Predictor
5 versions - Latest release: over 3 years ago - 1 dependent repositories - 56 downloads last month - 32 stars on GitHub - 1 maintainer
geofetch 0.12.6
Downloads data and metadata from GEO and SRA and creates standard PEPs.
22 versions - Latest release: 3 months ago - 1 dependent repositories - 444 downloads last month - 39 stars on GitHub - 3 maintainers
microhapulator 0.4.1
Software package for simulating and analyzing microhaplotype sequence data
1 version - Latest release: over 4 years ago - 1 dependent repositories - 9 downloads last month - 6 stars on GitHub - 1 maintainer
htsinfer 0.2.0
HTSinfer infers metadata from High Throughput Sequencing (HTS) data
1 version - Latest release: almost 4 years ago - 1 dependent repositories - 17 downloads last month - 8 stars on GitHub - 1 maintainer
Top 3.4% on pypi.org
deeptools 3.5.5
Useful tools for exploring deep sequencing data.
60 versions - Latest release: 2 months ago - 6 dependent packages - 36 dependent repositories - 2.33 thousand downloads last month - 645 stars on GitHub - 3 maintainers
pipestat 0.9.1
A pipeline results reporter
36 versions - Latest release: 22 days ago - 4 dependent packages - 3 dependent repositories - 25.9 thousand downloads last month - 4 stars on GitHub - 2 maintainers
bedhost 0.2.0
A database server application that provides both a RESTful API and GUI for access to BED files an...
4 versions - Latest release: 5 months ago - 65 downloads last month - 37,327 stars on GitHub - 2 maintainers
Top 7.8% on pypi.org
yacman 0.9.3
A standardized configuration object for reference genome assemblies
30 versions - Latest release: 3 months ago - 10 dependent packages - 47 dependent repositories - 38 thousand downloads last month - 7 stars on GitHub - 4 maintainers
svist4get 1.3.1
A simple visualization tool for genomic tracks from sequencing experiments
47 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 480 downloads last month - 2 stars on GitHub - 1 maintainer
sequana-rnaseq 0.19.3
A RNAseq pipeline from raw reads to feature counts
44 versions - Latest release: 3 months ago - 1 dependent repositories - 232 downloads last month - 17 stars on GitHub - 2 maintainers
sequana-pipetools 1.0.1
A set of tools to help building or using Sequana pipelines
69 versions - Latest release: about 1 month ago - 1 dependent package - 2 dependent repositories - 923 downloads last month - 2 stars on GitHub - 1 maintainer
sequana-fastqc 1.8.2
A multi-sample fastqc pipeline from Sequana project
35 versions - Latest release: 3 months ago - 1 dependent repositories - 275 downloads last month - 3 stars on GitHub - 1 maintainer
seq-ann 1.1.0
Sequence Annotation
3 versions - Latest release: over 4 years ago - 1 dependent package - 4 dependent repositories - 45 downloads last month - 5 stars on GitHub - 1 maintainer
pipestat-reader 0.0.3
A generator of pipestat-based APIs
2 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 20 downloads last month - 0 stars on GitHub - 2 maintainers
Top 4.7% on pypi.org
peppy 0.40.1
A python-based project metadata manager for portable encapsulated projects
58 versions - Latest release: 4 months ago - 9 dependent packages - 25 dependent repositories - 14.9 thousand downloads last month - 35 stars on GitHub - 4 maintainers
Top 7.0% on pypi.org
pairtools 1.1.0
CLI tools to process mapped Hi-C data
11 versions - Latest release: 23 days ago - 3 dependent packages - 4 dependent repositories - 322 downloads last month - 87 stars on GitHub - 2 maintainers
geniml 0.3.0
Genomic interval toolkit
3 versions - Latest release: about 1 month ago - 3 dependent packages - 388 downloads last month - 2 maintainers
Top 5.1% on pypi.org
galaxy-web-stack 24.0.2
Galaxy web stack abstraction
18 versions - Latest release: 9 days ago - 5 dependent packages - 10 dependent repositories - 437 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-web-apps 24.0.2
Galaxy web apps
15 versions - Latest release: 9 days ago - 2 dependent packages - 1 dependent repositories - 233 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: 9 days ago - 23 dependent packages - 23 dependent repositories - 16.7 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 1.6% on pypi.org
galaxy-tool-util 24.0.2
Galaxy tool and tool dependency utilities
60 versions - Latest release: 9 days ago - 16 dependent packages - 43 dependent repositories - 17.9 thousand downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 4.9% on pypi.org
galaxy-data 24.0.2
Galaxy datatype framework and datatypes
24 versions - Latest release: 9 days ago - 9 dependent packages - 13 dependent repositories - 782 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 2.1% on pypi.org
cooler 0.9.3
Sparse binary format for genomic interaction matrices.
45 versions - Latest release: 8 months ago - 22 dependent packages - 64 dependent repositories - 3.6 thousand downloads last month - 189 stars on GitHub - 2 maintainers
bioconvert 1.1.1
convert between bioinformatics formats
32 versions - Latest release: 10 months ago - 1 dependent package - 1 dependent repositories - 231 downloads last month - 350 stars on GitHub - 1 maintainer
cutseq 0.0.34 💰
Automatically cut adapter / barcode / UMI from NGS data
34 versions - Latest release: 15 days ago - 2.34 thousand downloads last month - 3 stars on GitHub - 1 maintainer
vfind 0.1.0
A simple variant finder for NGS data
1 version - Latest release: about 1 month ago - 84 downloads last month - 1 stars on GitHub - 1 maintainer
galaxy-tool-shed 24.0.2
Galaxy auth framework and implementations
4 versions - Latest release: 9 days ago - 102 downloads last month - 1,315 stars on GitHub - 1 maintainer
galaxy-schema 24.0.2
Galaxy auth framework and implementations
4 versions - Latest release: 9 days ago - 111 downloads last month - 1,315 stars on GitHub - 1 maintainer
bedboss 0.2.1
Pipelines for genomic region file to produce bed files, and it's statistics
6 versions - Latest release: about 1 month ago - 180 downloads last month - 1 stars on GitHub - 2 maintainers
galaxy-tours 24.0.2
Galaxy tours backend framework
15 versions - Latest release: 9 days ago - 1 dependent package - 362 downloads last month - 1,315 stars on GitHub - 1 maintainer
galaxy-navigation 24.0.2
Galaxy client DOM navigation framework
15 versions - Latest release: 9 days ago - 2 dependent packages - 417 downloads last month - 1,315 stars on GitHub - 1 maintainer
monte-barcode 0.0.2
Generating sets of random DNA sequences optimized for use in high-throughput sequencing.
3 versions - Latest release: 12 months ago - 32 downloads last month - 0 stars on GitHub - 1 maintainer
oxbow 0.3.1
Read specialized bioinformatic file formats into dataframes.
4 versions - Latest release: 4 months ago - 1 dependent package - 1 dependent repositories - 913 downloads last month - 39 stars on GitHub - 3 maintainers
strkit-rust-ext 0.10.0
A short tandem repeat (STR) genotyping and analysis toolkit for long reads
10 versions - Latest release: 3 months ago - 1 dependent package - 726 downloads last month - 2 stars on GitHub - 1 maintainer
zarp 0.1.1 removed
User-friendly command-line interface for the ZARP RNA-Seq analysis pipeline
1 version - Latest release: over 1 year ago - 1 maintainer
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 - 2 maintainers
sigalign 0.2.0
SigAlign's language binding for python
2 versions - Latest release: 11 months ago - 51 downloads last month - 10 stars on GitHub - 1 maintainer
pydemux 1.0.1
Python package for demultiplexing raw sequencing reads in SAM/BAM format
2 versions - Latest release: over 1 year ago - 22 downloads last month - 0 stars on GitHub - 1 maintainer
tecount 1.0.1
Count read alignments on transposable elements subfamilies, families and classes.
5 versions - Latest release: over 1 year ago - 40 downloads last month - 5 stars on GitHub - 1 maintainer
Top 5.4% on pypi.org
galaxy-files 24.0.2
Galaxy file source framework and default plugins
16 versions - Latest release: 9 days ago - 4 dependent packages - 6 dependent repositories - 499 downloads last month - 1,315 stars on GitHub - 3 maintainers
Top 6.1% on pypi.org
galaxy-config 24.0.2
Galaxy configuration
16 versions - Latest release: 9 days ago - 3 dependent packages - 3 dependent repositories - 393 downloads last month - 1,315 stars on GitHub - 3 maintainers
vcfwiper 2021.1.4
A package to wipe out uncompliant VCF files
1 version - Latest release: almost 3 years ago - 1 dependent repositories - 6 downloads last month - 1 maintainer
vcf2variants 1.3
A python tool to convert vcf to varda variant files.
7 versions - Latest release: 4 months ago - 1 dependent repositories - 35 downloads last month - 2 stars on GitHub - 1 maintainer
solida 0.9.7
NGS pipelines bootstrapper
23 versions - Latest release: over 3 years ago - 1 dependent repositories - 147 downloads last month - 4 stars on GitHub - 1 maintainer
sequana-pacbio-qc 1.0.1
QC on various type of pacbio data
5 versions - Latest release: 10 months ago - 1 dependent repositories - 15 downloads last month - 139 stars on GitHub - 1 maintainer
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 - 1 maintainer
seqann 1.0.0
Sequence Annotation
44 versions - Latest release: over 5 years ago - 1 dependent package - 1 dependent repositories - 203 downloads last month - 5 stars on GitHub - 1 maintainer
samsift 0.2.5
SAMsift - sift your alignments
6 versions - Latest release: about 6 years ago - 1 dependent repositories - 55 downloads last month - 21 stars on GitHub - 1 maintainer
rnftools 0.3.0
RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
19 versions - Latest release: about 7 years ago - 1 dependent repositories - 76 downloads last month - 14 stars on GitHub - 1 maintainer
rna-cd 0.2.0
RNA contamination detector
2 versions - Latest release: almost 5 years ago - 1 dependent repositories - 11 downloads last month - 2 stars on GitHub - 2 maintainers
riboplot 0.3.1 💰
Plot read counts of RiboSeq data from BAM format alignment files
11 versions - Latest release: about 7 years ago - 4 dependent repositories - 106 downloads last month - 4 stars on GitHub - 1 maintainer
rgt 1.0.2
Toolkit to perform regulatory genomics data analysis
30 versions - Latest release: 10 months ago - 1 dependent repositories - 134 downloads last month - 100 stars on GitHub - 3 maintainers
refgenieserver 0.7.0
This server provides both a web interface and a RESTful API. Users may explore and download archi...
15 versions - Latest release: about 3 years ago - 1 dependent repositories - 43 downloads last month - 3 maintainers
referenceseeker 1.8.0
ReferenceSeeker: rapid determination of appropriate reference genomes.
12 versions - Latest release: over 2 years ago - 1 dependent repositories - 130 downloads last month - 85 stars on GitHub - 1 maintainer
raisin.restyler 1.3
A package used in the Raisin web application
2 versions - Latest release: over 11 years ago - 2 dependent repositories - 3 downloads last month - 1 maintainer
raisin.recipe.load 1.1.2
A Buildout recipe for loading data into the Raisin data warehouse
1 version - Latest release: over 11 years ago - 2 dependent repositories - 9 downloads last month - 1 maintainer
raisin.recipe.extract 1.1.3
A Buildout recipe for loading data into the Raisin data warehouse
2 versions - Latest release: over 11 years ago - 2 dependent repositories - 11 downloads last month - 1 maintainer
raisin.box 1.4
A package used in the Raisin web application
2 versions - Latest release: over 11 years ago - 2 dependent repositories - 8 downloads last month - 0 stars on GitHub - 1 maintainer
raisin.page 1.3
A package used in the Raisin web application
1 version - Latest release: over 11 years ago - 2 dependent repositories - 7 downloads last month - 1 maintainer
pytest-ngsfixtures 0.8.1
pytest ngs fixtures
12 versions - Latest release: over 4 years ago - 2 dependent repositories - 120 downloads last month - 7 stars on GitHub - 1 maintainer
pygvcf2coverage 0.2
A python tool to extract coverage from gvcf files.
2 versions - Latest release: about 4 years ago - 1 dependent repositories - 13 downloads last month - 2 stars on GitHub - 1 maintainer
pygtftk 1.6.2
The Python GTF toolkit (pygtftk) package: easy handling of GTF files
26 versions - Latest release: about 2 years ago - 1 dependent repositories - 411 downloads last month - 41 stars on GitHub - 1 maintainer
pyflagstats 0.1.4
Efficient subroutines for computing summary statistics for the SAM FLAG field
5 versions - Latest release: over 4 years ago - 1 dependent repositories - 24 downloads last month - 15 stars on GitHub - 1 maintainer
pyconfdict 0.0.1.dev3
Python configuration dictionary
1 version - Latest release: over 8 years ago - 1 dependent repositories - 11 downloads last month - 14 stars on GitHub - 1 maintainer
pathogentrack 0.2.3
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data
1 version - Latest release: over 2 years ago - 1 dependent repositories - 23 downloads last month - 24 stars on GitHub - 1 maintainer
pararead 0.7.0
Parallel processing of sequencing reads
4 versions - Latest release: almost 5 years ago - 1 dependent package - 3 dependent repositories - 117 downloads last month - 8 stars on GitHub - 4 maintainers
palos 0.1.37
Misc Python modules developed and used by the yfish group
56 versions - Latest release: about 1 year ago - 1 dependent package - 1 dependent repositories - 259 downloads last month - 0 stars on GitHub - 1 maintainer
ore 0.2.1
Associate outliers with rare variation
34 versions - Latest release: over 5 years ago - 1 dependent repositories - 257 downloads last month - 1 stars on GitHub - 1 maintainer
ngs-toolkit 0.25.1
A toolkit for NGS analysis with Python.
31 versions - Latest release: over 3 years ago - 1 dependent repositories - 170 downloads last month - 13 stars on GitHub - 1 maintainer
ngs-test-utils 0.0.5
Utilities for generation of synthetic NGS files
5 versions - Latest release: almost 4 years ago - 1 dependent repositories - 47 downloads last month - 0 stars on GitHub - 4 maintainers
ngsci 0.0.1
The Next Generation Sequencing Complexity Index
1 version - Latest release: over 3 years ago - 1 dependent repositories - 9 downloads last month - 0 stars on GitHub - 1 maintainer
ngsderive 4.0.0
Forensic analysis tool useful in backwards computing information from next-generation sequencing ...
24 versions - Latest release: 7 months ago - 1 dependent repositories - 172 downloads last month - 11 stars on GitHub - 1 maintainer
nanosim-h 1.1.0.4
NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
5 versions - Latest release: almost 6 years ago - 1 dependent repositories - 33 downloads last month - 16 stars on GitHub - 1 maintainer
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 - 1 maintainer
mtags 1.0.4
mTAGs - taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA gene.
2 versions - Latest release: over 2 years ago - 1 dependent repositories - 10 downloads last month - 6 stars on GitHub - 1 maintainer
mitty 2.29.0
Simulator for genomic data
4 versions - Latest release: over 5 years ago - 1 dependent repositories - 27 downloads last month - 13 stars on GitHub - 1 maintainer
microhapdb 0.10.1
Portable database of microhaplotype marker and allele frequency data
13 versions - Latest release: 7 months ago - 1 dependent repositories - 87 downloads last month - 8 stars on GitHub - 1 maintainer
manorm 1.3.0
A robust model for quantitative comparison of ChIP-Seq data sets
7 versions - Latest release: about 4 years ago - 1 dependent repositories - 34 downloads last month - 20 stars on GitHub - 1 maintainer
loopercli 0.12.6
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
8 versions - Latest release: about 4 years ago - 3 dependent repositories - 43 downloads last month - 19 stars on GitHub - 4 maintainers
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 - 3 maintainers
grape.recipe.pipeline 1.1.16
A Buildout recipe installing Grape RNA-Seq pipelines
13 versions - Latest release: over 10 years ago - 3 dependent repositories - 16 downloads last month - 1 maintainer
grape.pipeline.runner 1.0
Console script for running Grape RNA-Seq pipelines
1 version - Latest release: over 11 years ago - 2 dependent repositories - 7 downloads last month - 0 stars on GitHub - 1 maintainer
Top 5.1% on pypi.org
galaxy-web-framework 24.0.2
Galaxy web framework
19 versions - Latest release: 9 days ago - 4 dependent packages - 10 dependent repositories - 423 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-test-tools 19.9.0.dev2
Galaxy Test Tools`
1 version - Latest release: over 2 years ago - 1 dependent repositories - 13 downloads last month - 1,315 stars on GitHub - 3 maintainers
galaxy-test-driver 24.0.2
Galaxy test driver
18 versions - Latest release: 9 days ago - 1 dependent package - 1 dependent repositories - 185 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: 9 days ago - 5 dependent packages - 10 dependent repositories - 430 downloads last month - 1,315 stars on GitHub - 3 maintainers
fqutils 0.0.0.dev6
fastq file utils in python
5 versions - Latest release: over 6 years ago - 1 dependent repositories - 22 downloads last month - 1 maintainer
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 - 1 maintainer
fastqwiper 2023.2.82
An ensamble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired rea...
19 versions - Latest release: 7 months ago - 1 dependent repositories - 46 downloads last month - 15 stars on GitHub - 1 maintainer
fastq-and-furious 0.3.2
Fast handling of FASTQ files
6 versions - Latest release: almost 3 years ago - 2 dependent repositories - 32 downloads last month - 50 stars on GitHub - 1 maintainer
Top 8.1% on pypi.org
eido 0.2.2
A project metadata validator
19 versions - Latest release: 6 months ago - 3 dependent packages - 6 dependent repositories - 13.9 thousand downloads last month - 4 stars on GitHub - 3 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 - 4 maintainers
demultiplex 1.2.2
Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes
9 versions - Latest release: over 2 years ago - 1 dependent repositories - 131 downloads last month - 27 stars on GitHub - 1 maintainer
demort 0.2.4
DEmultiplexing MOnitoring Report Tool
3 versions - Latest release: almost 5 years ago - 1 dependent repositories - 24 downloads last month - 0 stars on GitHub - 1 maintainer
crispresso 1.0.13
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data
11 versions - Latest release: almost 6 years ago - 1 dependent repositories - 62 downloads last month - 128 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 - 1 maintainer
circle-map 1.1.4
Circular DNA analysis tools
10 versions - Latest release: about 4 years ago - 1 dependent repositories - 94 downloads last month - 58 stars on GitHub - 1 maintainer
chronqc 1.0.4
A Quality Control Monitoring System for Clinical Next Generation Sequencing
4 versions - Latest release: over 6 years ago - 1 dependent repositories - 39 downloads last month - 17 stars on GitHub - 1 maintainer
chfilter 1.3
Simple instructions to remove 16s rRNA reads from metagenomics samples
2 versions - Latest release: about 6 years ago - 1 dependent repositories - 16 downloads last month - 0 stars on GitHub - 1 maintainer
checkqc 4.0.2
A simple program to parse Illumina NGS data and check it for quality criteria.
37 versions - Latest release: 24 days ago - 1 dependent repositories - 504 downloads last month - 24 stars on GitHub - 3 maintainers
Related Keywords
bioinformatics 114 sequencing 53 genomics 45 pipeline 44 workflow 41 hacktoberfest 30 dna 28 workflow-engine 27 science 27 usegalaxy 26 Galaxy 21 RNA-Seq 14 transcriptome 14 python 12 ETL 11 rna-seq 10 project 10 snakemake 8 NGS 7 metadata 6 metagenomics 6 fastq 6 sequana 5 chip-seq 5 galaxy 5 bed 4 GUI 4 wgs 4 hi-c 3 3d-genome 3 pipeline-submission-engine 3 python3 3 read-simulation 3 sequence-analysis 3 illumina 3 sequence 3 quality-control 3 pipelines 3 coverage 3 barcode 3 bacteria 3 microbiology 3 cnv 2 database 2 manager 2 conda 2 DNA 2 Hi-C 2 contact 2 atac-seq 2 bioinformatics-pipeline 2 dna-seq 2 ChIP-seq 2 conversion 2 nanopore 2 alignment 2 mapper-evaluation 2 ngs-format 2 sra 2 gvcf 2 forensics 2 microhaplotypes 2 high-throughput sequencing 2 sam 2 rna 2 reproducibility 2 bam 2 server 2 demultiplexing 2 reference-genome 2 hts 2 next-generation-sequencing 2 hla 2 RNAseq 2 hifi 2 RNADiff 2 differential analysis 2 long-reads 2 long-read-sequencing 2 seqann 2 hla-typing 2 gfe 2 filtering 1 validation 1 cancer-genomics 1 cancer 1 RNA 1 multithreading 1 parallelization 1 pypi-package 1 vizualisation 1 snvs 1 variants 1 corrupted 1 pep 1 fasta 1 jsonschema 1 recovery 1 fix 1 demultiplex 1