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
slamdunk 0.4.3
SLAMdunk suite for analyzing SLAM-seq data12 versions - Latest release: about 4 years ago - 1 dependent repositories - 89 downloads last month - 36 stars on GitHub - 1 maintainer
assnake 0.8.9
System for metagenomics data analysis8 versions - Latest release: about 4 years ago - 1 dependent repositories - 51 downloads last month - 11 stars on GitHub - 1 maintainer
Top 2.0% on pypi.org
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
multiqc 1.10.1
Create aggregate bioinformatics analysis reports across many samples and tools34 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
bio-aid 0.3.1
Genetic Analysis Tools22 versions - Latest release: 8 months ago - 26 downloads last month - 1 maintainer
Top 4.3% on pypi.org
48 versions - Latest release: 2 days ago - 1 dependent package - 4 dependent repositories - 9.17 thousand downloads last month - 216 stars on GitHub - 4 maintainers
nf-core 2.14.1
Helper tools for use with nf-core Nextflow pipelines.48 versions - Latest release: 2 days ago - 1 dependent package - 4 dependent repositories - 9.17 thousand downloads last month - 216 stars on GitHub - 4 maintainers
assnake-core-preprocessing 0.5.2
Reads preprocessing module for assnake2 versions - Latest release: about 4 years ago - 1 dependent repositories - 24 downloads last month - 0 stars on GitHub - 1 maintainer
sequana-mapper 1.2.1
A multi-sample mapper to map reads onto a reference24 versions - Latest release: 3 months ago - 1 dependent repositories - 85 downloads last month - 5 stars on GitHub - 2 maintainers
smallgenomeutilities 0.4.0
A collection of scripts that are useful for dealing with viral RNA NGS data.5 versions - Latest release: 9 months ago - 1 dependent repositories - 44 downloads last month - 10 stars on GitHub - 6 maintainers
massgenotyping 0.2.2
Python package for microsatellite genotyping from amplicon sequencing data5 versions - Latest release: 4 months ago - 1 dependent repositories - 40 downloads last month - 7 stars on GitHub - 2 maintainers
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
vfind 0.1.0
A simple variant finder for NGS data1 version - Latest release: 26 days ago - 84 downloads last month - 1 stars on GitHub - 2 maintainers
biosniff 1.0.0
A sniffer for biological data formats5 versions - Latest release: over 1 year ago - 2 dependent repositories - 118 downloads last month - 3 stars on GitHub - 2 maintainers
sequdas-qc 1.0.1
Sequence Upload and Data Archiving System2 versions - Latest release: over 4 years ago - 1 dependent repositories - 7 downloads last month - 0 stars on GitHub - 2 maintainers
sequana-revcomp 1.1.0
reverse complement a set of FastQ files8 versions - Latest release: 5 months ago - 1 dependent repositories - 14 downloads last month - 0 stars on GitHub - 2 maintainers
custardpy 0.7.2
Hi-C analysis tools by Python351 versions - Latest release: 2 months ago - 232 downloads last month - 3 stars on GitHub - 2 maintainers
pysalsa 0.1.0
convert between bioinformatics formats1 version - Latest release: about 2 years ago - 1 dependent repositories - 14 downloads last month - 0 stars on GitHub - 2 maintainers
freebarcodes 3.1.0
FREE Divergence Error-Correcting DNA Barcodes7 versions - Latest release: over 1 year ago - 1 dependent repositories - 33 downloads last month - 20 stars on GitHub - 1 maintainer
Top 9.3% on pypi.org
2 versions - Latest release: about 5 years ago - 2 dependent repositories - 405 downloads last month - 2 maintainers
sequenza-utils 3.0.0
Analysis of cancer sequencing samples, utilities for the sequenza R package2 versions - Latest release: about 5 years ago - 2 dependent repositories - 405 downloads last month - 2 maintainers
sequana-fastqc 1.8.2
A multi-sample fastqc pipeline from Sequana project35 versions - Latest release: 3 months ago - 1 dependent repositories - 239 downloads last month - 3 stars on GitHub - 2 maintainers
samsift 0.2.5
SAMsift - sift your alignments6 versions - Latest release: about 6 years ago - 1 dependent repositories - 55 downloads last month - 21 stars on GitHub - 2 maintainers
iannotatesv 1.2.1
The module helps to annotate structural variants called using NGS on human.2 versions - Latest release: over 3 years ago - 1 dependent repositories - 27 downloads last month - 16 stars on GitHub - 2 maintainers
goenrichment 1.0.3
GO enrichment analysis from a list of gene names using a precomputed database10 versions - Latest release: over 2 years ago - 3 dependent repositories - 99 downloads last month - 0 stars on GitLab.com - 2 maintainers
iridauploader 0.9.2
IRIDA uploader: upload NGS data to IRIDA system16 versions - Latest release: 12 months ago - 1 dependent repositories - 149 downloads last month - 8 stars on GitHub - 4 maintainers
de-toolkit 0.9.12
Suite of tools for working with count data29 versions - Latest release: over 4 years ago - 1 dependent repositories - 169 downloads last month - 2 maintainers
jupyterngsplugin 0.0.13a3
Jupyter notebook plugin for Bioinformatics NGS data analysis9 versions - Latest release: about 4 years ago - 2 dependent repositories - 76 downloads last month - 0 stars on GitLab.com - 1 maintainer
cutseq 0.0.34 💰
Automatically cut adapter / barcode / UMI from NGS data34 versions - Latest release: 10 days ago - 2.34 thousand downloads last month - 3 stars on GitHub - 2 maintainers
vcftoolz 1.2.3
Tools for working with Variant Call Format files.7 versions - Latest release: 11 months ago - 1 dependent repositories - 125 downloads last month - 8 stars on GitHub - 4 maintainers
prophyle 0.1.0
ProPhyle metagenomic classifier54 versions - Latest release: about 7 years ago - 1 dependent repositories - 918 downloads last month - 31 stars on GitHub - 2 maintainers
sequana-variant-calling 1.2.0
A multi-sample variant calling pipeline24 versions - Latest release: 3 months ago - 1 dependent repositories - 104 downloads last month - 0 stars on GitHub - 1 maintainer
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
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
fastcontext 2022.8.30
A tool for identification of adapters and other sequence patterns in the next generation sequenci...3 versions - Latest release: over 1 year ago - 9 downloads last month - 2 stars on GitHub - 2 maintainers
mvirs 1.1.1
mVIRs: Localisation of inducible prophages using NGS data1 version - Latest release: about 2 years ago - 1 dependent repositories - 8 downloads last month - 12 stars on GitHub - 2 maintainers
sequana-denovo 0.10.0
Multi-sample denovo assembly of FastQ sequences (short read)8 versions - Latest release: 5 months ago - 1 dependent repositories - 45 downloads last month - 3 stars on GitHub - 2 maintainers
geo-upload-tool 1.0.8
CLI tool for preparing data submission to Gene Expression Omnibus9 versions - Latest release: almost 3 years ago - 1 dependent repositories - 65 downloads last month - 2 maintainers
fdstools 2.0.4
Forensic DNA Sequencing Tools13 versions - Latest release: about 1 year ago - 2 dependent repositories - 363 downloads last month - 5 stars on GitHub - 1 maintainer
seqtables 0.11
Package for efficient analysis of next generation sequencing amplicon data using numpy and datafr...2 versions - Latest release: over 4 years ago - 1 dependent repositories - 12 downloads last month - 5 stars on GitHub - 2 maintainers
metatrim 1.0.4
Trim reads from metabarcoding libraries5 versions - Latest release: almost 2 years ago - 49 downloads last month - 2 maintainers
strnaming 1.2.0
STRNaming STR Sequence Nomenclature8 versions - Latest release: 4 months ago - 1 dependent package - 1 dependent repositories - 134 downloads last month - 1 stars on GitHub - 2 maintainers
sequana-downsampling 0.9.0
downsample NGS data sets5 versions - Latest release: over 1 year ago - 1 dependent repositories - 18 downloads last month - 0 stars on GitHub - 2 maintainers
freediv10xcellbcs 0.0a1
FREE divergence-based decoding of 10X cell barcodes1 version - Latest release: over 1 year ago - 7 downloads last month - 0 stars on GitHub - 2 maintainers
gostrat 0.0.8
Tool to stratify GO terms based on first significant parent8 versions - Latest release: almost 4 years ago - 1 dependent repositories - 64 downloads last month - 2 maintainers
pasio 1.1.2
Pasio is a tool for segmentation and denosing DNA coverage profiles coming from high-throughput s...4 versions - Latest release: over 4 years ago - 1 dependent repositories - 44 downloads last month - 1 stars on GitHub - 2 maintainers
mirge3 0.1.4
Comprehensive analysis of small RNA sequencing Data14 versions - Latest release: about 1 year ago - 1 dependent repositories - 146 downloads last month - 25 stars on GitHub - 1 maintainer
seqcluster 1.2.8
Small RNA-seq pipeline39 versions - Latest release: about 3 years ago - 3 dependent repositories - 75 downloads last month - 35 stars on GitHub - 1 maintainer
sequana-bioconvert 1.1.0
description: convert NGS format from one to another using bioconvert5 versions - Latest release: 5 months ago - 1 dependent repositories - 18 downloads last month - 1 stars on GitHub - 2 maintainers
ngs-analysis 0.0.6
Analyze deep sequencing of complex libraries6 versions - Latest release: 3 months ago - 34 downloads last month - 0 stars on GitHub - 1 maintainer
hydra-genetics 2.0.0
Helper tools for use with hydra-genetics pipelines.60 versions - Latest release: 16 days ago - 23 dependent repositories - 2.11 thousand downloads last month - 3 stars on GitHub - 2 maintainers
sequana-sphinxext 1.0.0
A set of sphinx extension for Sequana pipelines, wrappers and rules3 versions - Latest release: over 2 years ago - 1 dependent repositories - 27 downloads last month - 0 stars on GitHub - 2 maintainers
crispr-cas9 0.3.4
script for indels counting in sequencing data6 versions - Latest release: almost 3 years ago - 1 dependent repositories - 23 downloads last month - 4 stars on GitHub - 2 maintainers
sequana-depletion 0.3.0
A pipeline to deplete reads from a given reference3 versions - Latest release: 5 months ago - 1 dependent repositories - 17 downloads last month - 1 stars on GitHub - 2 maintainers
sequana-multitax 0.12.1
A multi-sample and multi-databases taxonomic analysis using Kraken12 versions - Latest release: 5 months ago - 1 dependent repositories - 32 downloads last month - 2 maintainers
solida 0.9.7
NGS pipelines bootstrapper23 versions - Latest release: over 3 years ago - 1 dependent repositories - 147 downloads last month - 4 stars on GitHub - 2 maintainers
multiqc-jupyterlab-helper 1.12.1.dev0
Create aggregate bioinformatics analysis reports across many samples and tools2 versions - Latest release: over 2 years ago - 1 dependent repositories - 12 downloads last month - 1,162 stars on GitHub - 2 maintainers
multiqc-msk 1.11.dev0
Create aggregate bioinformatics analysis reports across many samples and tools1 version - Latest release: almost 3 years ago - 1 dependent repositories - 14 downloads last month - 1,162 stars on GitHub - 2 maintainers
bacpage 2024.3.8
An easy-to-use pipeline for the assembly and analysis of bacterial genomes3 versions - Latest release: 2 months ago - 20 downloads last month - 7 stars on GitHub - 2 maintainers
telomerehunter 1.1.0
Estimation of Telomere Content from WGS Data6 versions - Latest release: over 5 years ago - 2 dependent repositories - 65 downloads last month - 4 maintainers
anacore 3.1.0
Libraries for managing standard file formats and objects from NGS.11 versions - Latest release: about 2 months ago - 1 dependent repositories - 105 downloads last month - 3 stars on GitHub - 1 maintainer
mirge-build 0.0.1
miRge-build: Building libraries of small RNA sequencing Data1 version - Latest release: over 3 years ago - 1 dependent repositories - 8 downloads last month - 2 stars on GitHub - 2 maintainers
megaqc 0.2.0
Collect and visualise data across multiple MultiQC runs2 versions - Latest release: over 3 years ago - 1 dependent repositories - 25 downloads last month - 93 stars on GitHub - 2 maintainers
pymasc 0.3.2
Python implementation to calc mappability-sensitive cross-correlation for fragment length estimat...12 versions - Latest release: over 4 years ago - 1 dependent repositories - 10 downloads last month - 2 stars on GitHub - 2 maintainers
sequana-pacbio-qc 1.0.1
QC on various type of pacbio data5 versions - Latest release: 10 months ago - 1 dependent repositories - 15 downloads last month - 139 stars on GitHub - 2 maintainers
counhto 1.1.0
Python package for generating and demultiplexing hash tag oligo count matrices from cellranger ou...2 versions - Latest release: about 1 year ago - 13 downloads last month - 0 stars on GitHub - 2 maintainers
bioconvert 1.1.1
convert between bioinformatics formats32 versions - Latest release: 10 months ago - 1 dependent repositories - 231 downloads last month - 350 stars on GitHub - 1 maintainer
Top 5.1% on pypi.org
97 versions - Latest release: about 2 months ago - 7 dependent packages - 14 dependent repositories - 788 downloads last month - 0 stars on GitHub - 1 maintainer
sequana 0.16.11
A set of standalone application and pipelines dedicated to NGS analysis97 versions - Latest release: about 2 months ago - 7 dependent packages - 14 dependent repositories - 788 downloads last month - 0 stars on GitHub - 1 maintainer
multiqc-sgr 1.21.3
Create aggregate bioinformatics analysis reports across many samples and tools7 versions - Latest release: 24 days ago - 570 downloads last month - 0 stars on GitHub - 1 maintainer
sequana-quality-control 0.10.0
A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix),...5 versions - Latest release: about 2 years ago - 1 dependent repositories - 13 downloads last month - 0 stars on GitHub - 2 maintainers
irida-uploader-cl 0.2
IRIDA uploader: upload NGS data to IRIDA system2 versions - Latest release: over 4 years ago - 1 dependent repositories - 1 downloads last month - 0 stars on GitHub - 2 maintainers
c3s 1.0.0
Python Modules for XXXXXXXX1 version - Latest release: over 6 years ago - 16 downloads last month - 1 maintainer
varbscore 1.0.3
A python package to calculate varBscore using vcf input4 versions - Latest release: about 3 years ago - 1 dependent repositories - 6 downloads last month - 0 stars on GitHub - 2 maintainers
gmarrayfilter 1.0.3
A python package to filter SNP array data4 versions - Latest release: over 2 years ago - 1 dependent repositories - 14 downloads last month - 2 maintainers
cirrus-ngs 1.0.0a1
Cloud-optimized primary analysis pipelines for RNA-seq, miRNA-seq, ChIP-seq, and variant calling ...1 version - Latest release: almost 6 years ago - 1 dependent repositories - 9 downloads last month - 8 stars on GitHub - 2 maintainers
papolarity 1.1.2
Papolarity is a tool to analyze polarity of transcriptomic alignments such as Ribo-seq and RNA-seq.21 versions - Latest release: over 2 years ago - 1 dependent repositories - 32 downloads last month - 1 stars on GitHub - 2 maintainers
pycircos 1.0.2
This Tools is Design for NGS Circos Plot with using Python.2 versions - Latest release: over 4 years ago - 1 dependent repositories - 180 downloads last month - 5 stars on GitHub - 2 maintainers
Related Keywords
bioinformatics
34
sequencing
20
snakemake
16
sequana
11
biology
10
next generation sequencing
9
python
8
ngs
7
analysis
6
quality control
5
pipeline
5
pypi
5
quality-control
4
alignment
4
bwa
4
DNA
4
multiqc
3
data-visualization
3
reporting
3
bioconda
3
seqera
3
vizualisation
3
metagenomics
3
workflow
3
rna-seq
3
coverage
3
minimap2
3
REviewer
2
barcode
2
STRs
2
curation
2
RNA-seq
2
uploader
2
IRIDA
2
Jupyter
2
read visualization
2
machine learning
2
STR
2
MPS
2
forensics
2
denovo
2
assembly
2
sequence
2
read
2
tumor
2
bacteria
2
SNP
2
Reseq
2
phylogeny
2
ILLUMINA
2
METAGENOMIC
2
DATA
2
Python
2
barcodes
2
bio
2
genomics
2
small RNA analysis
2
bioinformatics tools
2
taxonomy
2
ngs-analysis
2
SAM
2
python3
1
dna-sequences
1
Next-Generation-Sequencing
1
virology
1
depletion
1
kraken
1
pipeline deployment
1
ansible
1
ngs-pipeline
1
bam2bed
1
fastq
1
downsampling
1
10X
1
segmentation
1
denoise
1
miRge
1
GUI
1
miRNA
1
snoRNA
1
mirna
1
report
1
smallrna
1
trna
1
convertion
1
bioconvert
1
library
1
variant
1
hydra-genetics
1
clinical
1
indels
1
crispr-cas9
1
deep-sequencing
1
fastq2fasta
1
bam2sam
1
conversion
1
bam2cram
1
bcf2vcf
1
bigbed2bed
1
convertor
1