Ecosyste.ms: Packages

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

pypi.org "nanopore" keyword

dajin2 0.4.5
One-step genotyping tools for targeted long-read sequencing
45 versions - Latest release: 22 days ago - 376 downloads last month - 4 stars on GitHub - 1 maintainer
surpyvor 0.15.0
Manipulate vcf files of structural variants using SURVIVOR
10 versions - Latest release: 11 months ago - 1 dependent repositories - 47 downloads last month - 18 stars on GitHub - 1 maintainer
pyguppyclient 0.1.0
Python client library for Guppy
11 versions - Latest release: almost 3 years ago - 1 dependent package - 1 dependent repositories - 85 downloads last month - 30 stars on GitHub - 1 maintainer
fast5purge 0.2.0
Remove sensible content from a fast5 file or directory
4 versions - Latest release: over 5 years ago - 1 dependent repositories - 24 downloads last month - 2 stars on GitHub - 1 maintainer
Top 7.5% on pypi.org
vbz-h5py-plugin 1.0.1
Oxford Nanopore Technologies VBZ HDF plugin for h5py
2 versions - Latest release: over 1 year ago - 4 dependent packages - 1 dependent repositories - 8.11 thousand downloads last month - 38 stars on GitHub - 1 maintainer
squigualiser 0.6.3
Visualise ONT raw signals
10 versions - Latest release: 10 days ago - 1 dependent package - 120 downloads last month - 95 stars on GitHub - 1 maintainer
Top 6.7% on pypi.org
sniffles 2.3.3
A fast structural variation caller for long-read sequencing data
12 versions - Latest release: 9 days ago - 1 dependent package - 3 dependent repositories - 769 downloads last month - 511 stars on GitHub - 3 maintainers
Top 8.5% on pypi.org
pyspoa 0.2.1
Python bindings to spoa
14 versions - Latest release: 7 months ago - 3 dependent packages - 4 dependent repositories - 1.44 thousand downloads last month - 12 stars on GitHub - 2 maintainers
pyslow5 1.1.0
slow5lib python bindings
14 versions - Latest release: 9 months ago - 4 dependent packages - 1 dependent repositories - 370 downloads last month - 35 stars on GitHub - 2 maintainers
Top 4.5% on pypi.org
pod5 0.3.10
Oxford Nanopore Technologies Pod5 File Format Python API and Tools
22 versions - Latest release: about 2 months ago - 7 dependent packages - 2 dependent repositories - 10 thousand downloads last month - 108 stars on GitHub - 1 maintainer
Top 3.8% on pypi.org
ont-fast5-api 4.1.3
Oxford Nanopore Technologies fast5 API software
37 versions - Latest release: 3 months ago - 9 dependent packages - 26 dependent repositories - 7.28 thousand downloads last month - 142 stars on GitHub - 1 maintainer
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 - 1.64 thousand downloads last month - 388 stars on GitHub - 1 maintainer
pistis 0.3.4
Quality control plotting for long reads
11 versions - Latest release: about 3 years ago - 1 dependent repositories - 53 downloads last month - 10 stars on GitHub - 1 maintainer
Top 8.9% on pypi.org
ont-bonito 0.7.3
A PyTorch Basecaller for Oxford Nanopore Reads
48 versions - Latest release: 5 months ago - 1 dependent repositories - 573 downloads last month - 374 stars on GitHub - 1 maintainer
ont-bonito-cuda113 0.5.3
A PyTorch Basecaller for Oxford Nanopore Reads
6 versions - Latest release: almost 2 years ago - 1 dependent repositories - 36 downloads last month - 374 stars on GitHub - 1 maintainer
ont-bonito-cuda111 0.5.3
A PyTorch Basecaller for Oxford Nanopore Reads
11 versions - Latest release: almost 2 years ago - 1 dependent repositories - 75 downloads last month - 372 stars on GitHub - 1 maintainer
chiron 0.6.1
A deep neural network basecaller for nanopore sequencing.
14 versions - Latest release: over 4 years ago - 109 downloads last month - 120 stars on GitHub - 1 maintainer
sequali 0.8.0
Sequali is a QC tool that generates useful graphs for both short and long-read data.
11 versions - Latest release: 7 days ago - 1.91 thousand downloads last month - 0 stars on GitHub - 1 maintainer
blue-crab 0.1.0
blue-crab: A Slow5/Blow5 <-> Pod5 converter
1 version - Latest release: 9 months ago - 38 downloads last month - 19 stars on GitHub - 2 maintainers
xron 1.0.7
A deep neural network basecaller for nanopore sequencing.
10 versions - Latest release: 7 months ago - 48 downloads last month - 11 stars on GitHub - 1 maintainer
pynanolab 3.0.3
A data analysis and visualization software
4 versions - Latest release: 7 months ago - 38 downloads last month - 10 stars on GitHub - 1 maintainer
nanomix 0.2.0
Methods for cell type deconvolution from Oxford Nanopore methylation calling
3 versions - Latest release: about 1 year ago - 42 downloads last month - 10 stars on GitHub - 1 maintainer
Top 7.9% on pypi.org
lib-pod5 0.3.10
Python bindings for the POD5 file format
22 versions - Latest release: about 2 months ago - 1 dependent package - 1 dependent repositories - 12.3 thousand downloads last month - 108 stars on GitHub - 1 maintainer
trackcluster 0.1.6
RNA-seq analysis for Long read RNA sequencing
5 versions - Latest release: over 1 year ago - 8 downloads last month - 10 stars on GitHub - 1 maintainer
lafite 1.0.2
Nanopore Direct RNA-seq Transcriptome Assembly
4 versions - Latest release: over 1 year ago - 1 dependent repositories - 16 downloads last month - 3 stars on GitHub - 1 maintainer
pod5-format-tools 0.0.41
Tools for use with the POD5 file format
9 versions - Latest release: over 1 year ago - 2 dependent repositories - 117 downloads last month - 108 stars on GitHub - 1 maintainer
mkr-format-tools 0.0.13
Tools for use with the MKR file format
4 versions - Latest release: almost 2 years ago - 1 dependent repositories - 30 downloads last month - 1 maintainer
xpore 0.5.6
xpore is a python package for Nanopore data analysis of differential RNA modifications.
11 versions - Latest release: over 3 years ago - 1 dependent repositories - 140 downloads last month - 127 stars on GitHub - 1 maintainer
variantbreak 1.0.4
Structural variant analyzer for data visualization on VariantMap
2 versions - Latest release: over 3 years ago - 1 dependent repositories - 12 downloads last month - 3 stars on GitHub - 1 maintainer
taeper 0.1.0
Simulate repeating a nanopore experiment.
1 version - Latest release: about 6 years ago - 1 dependent repositories - 16 downloads last month - 18 stars on GitHub - 1 maintainer
seamlessf5 0.2
Helpers for smoother transitioning to multi-read FAST5 files
2 versions - Latest release: over 5 years ago - 1 dependent repositories - 25 downloads last month - 6 stars on GitHub - 1 maintainer
plasmidpredictor 0.1.0
plasmidpredictor: predict which plasmid should be present from uncorrected long read data
1 version - Latest release: over 5 years ago - 1 dependent repositories - 48 downloads last month - 37 stars on GitHub - 1 maintainer
picopore 1.2.0
A tool for reducing the size of Oxford Nanopore Technologies' datasets without losing information.
21 versions - Latest release: over 6 years ago - 1 dependent repositories - 69 downloads last month - 31 stars on GitHub - 1 maintainer
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 - 1 maintainer
nanovar 1.6.2
Structural variant caller using low-depth long reads
23 versions - Latest release: 16 days ago - 1 dependent repositories - 151 downloads last month - 31 stars on GitHub - 1 maintainer
nanosv 1.2.4
Structural variation detection tool for Oxford Nanopore data.
12 versions - Latest release: over 4 years ago - 1 dependent repositories - 50 downloads last month - 86 stars on GitHub - 1 maintainer
nanostat 1.6.0
Calculate statistics for Oxford Nanopore sequencing data and alignments
28 versions - Latest release: over 2 years ago - 2 dependent repositories - 185 downloads last month - 78 stars on GitHub - 1 maintainer
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 - 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
nanoraw 0.4.2
Analysis of nanopore sequencing data.
8 versions - Latest release: 8 months ago - 1 dependent repositories - 16 downloads last month - 46 stars on GitHub - 1 maintainer
nanoqc 0.9.4
Create fastQC-like plots for Oxford Nanopore sequencing data
17 versions - Latest release: almost 4 years ago - 1 dependent repositories - 179 downloads last month - 81 stars on GitHub - 1 maintainer
nanoplotter 1.10.0
Plotting functions of Oxford Nanopore sequencing data
99 versions - Latest release: almost 5 years ago - 1 dependent package - 2 dependent repositories - 273 downloads last month - 2 stars on GitHub - 1 maintainer
nanopack 1.1.0
Install all Oxford Nanopore scrips and modules for processing and analysis
9 versions - Latest release: almost 4 years ago - 1 dependent repositories - 112 downloads last month - 189 stars on GitHub - 1 maintainer
Top 8.7% on pypi.org
nanomath 1.3.0
A few simple math function for other Oxford Nanopore processing scripts
47 versions - Latest release: about 1 year ago - 1 dependent package - 13 dependent repositories - 871 downloads last month - 9 stars on GitHub - 1 maintainer
nanolyse 1.2.1
Removing reads mapping to the lambda genome
18 versions - Latest release: over 1 year ago - 1 dependent repositories - 144 downloads last month - 27 stars on GitHub - 1 maintainer
Top 9.3% on pypi.org
nanofilt 2.8.0
Filtering and trimming of Oxford Nanopore Sequencing data
34 versions - Latest release: about 3 years ago - 2 dependent repositories - 311 downloads last month - 176 stars on GitHub - 1 maintainer
nanocomp 1.23.1
Comparing runs of Oxford Nanopore sequencing data and alignments
71 versions - Latest release: 11 months ago - 254 downloads last month - 88 stars on GitHub - 1 maintainer
minfq 1.4.7
Command line interface for uploading fastq files and monitoring minKNOW for minotour.
27 versions - Latest release: about 2 years ago - 1 dependent repositories - 269 downloads last month - 10 stars on GitHub - 3 maintainers
methplotlib 0.20.1
Plot methylation data obtained from nanopolish
17 versions - Latest release: about 2 years ago - 1 dependent repositories - 39 downloads last month - 84 stars on GitHub - 1 maintainer
Top 6.0% on pypi.org
medaka 1.11.3
Neural network sequence error correction.
85 versions - Latest release: 5 months ago - 3 dependent repositories - 1.28 thousand downloads last month - 383 stars on GitHub - 1 maintainer
medaka-cpu 1.11.3
Neural network sequence error correction.
39 versions - Latest release: 5 months ago - 1 dependent repositories - 600 downloads last month - 383 stars on GitHub - 1 maintainer
mccloud-cli 0.0.8
A command line to assist McCloud users.
8 versions - Latest release: over 2 years ago - 1 dependent repositories - 36 downloads last month - 269 stars on GitHub - 2 maintainers
lrplots 0.7.0
Plot collection for Long Read Sequencing
8 versions - Latest release: about 1 year ago - 1 dependent repositories - 48 downloads last month - 12 stars on GitHub - 1 maintainer
imgtools 0.2.0
Some tools for manipulating image files
2 versions - Latest release: over 6 years ago - 1 dependent repositories - 23 downloads last month - 1 stars on GitHub - 1 maintainer
fastqmetrics 0.1.0
Het hoeft voor
1 version - Latest release: over 6 years ago - 1 dependent repositories - 10 downloads last month - 0 stars on GitHub - 1 maintainer
fastq-anonymous 1.0.1
Change the sequence of a fastq file to enable sharing of confidential information, for troublesho...
2 versions - Latest release: over 6 years ago - 1 dependent repositories - 7 downloads last month - 0 stars on GitHub - 1 maintainer
deepsignal-plant 0.1.6
A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads ...
7 versions - Latest release: almost 2 years ago - 1 dependent repositories - 29 downloads last month - 51 stars on GitHub - 1 maintainer
deepsignal 0.2.0
A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads
11 versions - Latest release: about 2 years ago - 1 dependent repositories - 40 downloads last month - 105 stars on GitHub - 1 maintainer
mosaic-nist 1.3.5
A Modular Single-Molecule Analysis Interface.
16 versions - Latest release: over 6 years ago - 2 dependent repositories - 111 downloads last month - 37 stars on GitHub - 1 maintainer
nanocompore 1.0.4
Software package that identifies raw signal changes between two conditions from https://github.co...
6 versions - Latest release: almost 3 years ago - 1 dependent repositories - 77 downloads last month - 74 stars on GitHub - 1 maintainer
pepper-polish 0.1.5
RNN based standalone assembly polisher.
8 versions - Latest release: over 3 years ago - 1 dependent repositories - 63 downloads last month - 230 stars on GitHub - 1 maintainer
Top 7.8% on pypi.org
ont-remora 3.1.0
Nanopore methylation/modified base calling detached from basecalling
13 versions - Latest release: 5 months ago - 3 dependent repositories - 543 downloads last month - 139 stars on GitHub - 1 maintainer
Top 9.1% on pypi.org
pod5-format 0.0.41
Python bindings for the POD5 file format
10 versions - Latest release: over 1 year ago - 1 dependent package - 2 dependent repositories - 630 downloads last month - 108 stars on GitHub - 1 maintainer
poreplex 0.4.1
A versatile sequence read processor for nanopore direct RNA sequencing
7 versions - Latest release: about 5 years ago - 1 dependent repositories - 126 downloads last month - 77 stars on GitHub - 1 maintainer
pycoqc 2.5.2
PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies seque...
50 versions - Latest release: over 3 years ago - 579 downloads last month - 235 stars on GitHub - 1 maintainer
ampligone 1.3.1
Ampligone is a tool which accurately removes primer sequences from FastQ NGS reads in an amplicon...
9 versions - Latest release: about 1 month ago - 65 downloads last month - 8 stars on GitHub - 3 maintainers
recentrifuge 1.14.0
Robust comparative analysis and contamination removal for metagenomics
82 versions - Latest release: 3 months ago - 1 dependent repositories - 477 downloads last month - 83 stars on GitHub - 1 maintainer
mkr-format 0.0.13
Python bindings for the MKR file format
4 versions - Latest release: almost 2 years ago - 1 dependent repositories - 161 downloads last month - 1 maintainer
fast5seek 0.1.1
Get paths for fast5 files contained in BAM, SAM, or fastq.
2 versions - Latest release: over 5 years ago - 1 dependent repositories - 20 downloads last month - 11 stars on GitHub - 1 maintainer
tbpore 0.7.0
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
11 versions - Latest release: 7 months ago - 1 dependent repositories - 65 downloads last month - 11 stars on GitHub - 1 maintainer
acidoseq 1.3.7
Studying Acidobacteria reads
10 versions - Latest release: over 5 years ago - 1 dependent repositories - 48 downloads last month - 0 stars on GitHub - 1 maintainer
tiptoft 1.0.2
tiptoft: predict which plasmid should be present from uncorrected long read data
6 versions - Latest release: over 4 years ago - 1 dependent repositories - 52 downloads last month - 37 stars on GitHub - 1 maintainer
methylink 0.6.0
methylink is a tool to link methylation tags between SAM/BAM files.
6 versions - Latest release: 6 months ago - 36 downloads last month - 1 stars on GitHub - 1 maintainer
Top 7.9% on pypi.org
nanoget 1.19.3
Functions to extract information from Oxford Nanopore sequencing data and alignments.
70 versions - Latest release: 8 months ago - 1 dependent package - 13 dependent repositories - 1.09 thousand downloads last month - 11 stars on GitHub - 1 maintainer
bio-anglerfish 0.6.1
Anglerfish, a tool to demultiplex Illumina libraries from ONT data
6 versions - Latest release: 3 months ago - 1 dependent repositories - 44 downloads last month - 1 stars on GitHub - 1 maintainer
ont-guppy-duplex-pipeline 1.0.3
Oxford Nanopore Technologies duplex pipeline scripts for guppy
4 versions - Latest release: over 1 year ago - 1 dependent repositories - 24 downloads last month - 1 maintainer
deepsignal2 0.1.3
A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads
4 versions - Latest release: almost 2 years ago - 1 dependent repositories - 17 downloads last month - 25 stars on GitHub - 1 maintainer
Related Keywords
sequencing 19 bioinformatics 16 plotting 9 quality 8 control 8 basecalling 6 python 6 methylation 6 neural network 5 genomics 5 fast5 5 processing 5 pacbio 5 oxford-nanopore 4 pytorch 4 file-format 4 apache-arrow 4 rna-seq 3 long-reads 3 nanopore-sequencing 3 analysis 3 slow5 3 infectious-diseases 2 variant-calling 2 global-health 2 bioinformatics-pipeline 2 simulation 2 long read 2 nanovar 2 sv 2 rna-modifications 2 long-read 2 Nanopore 2 demultiplexing 2 python3 2 fastq 2 kmer 2 medaka 2 pathogen 2 ngs 2 filtering 2 trimming 2 statistics 2 epigenetics 2 plasmid 2 plasmidfinder 2 research 2 uncorrected 2 high-throughput 2 genome 2 correction 2 guppy 2 pod5 2 compression 2 hdf5 2 signal 2 basecaller 2 illumina 2 longread 2 duplex 1 amplicon-sequencing 1 jupyter-notebook 1 generates-plots 1 computing-metrics 1 multiplexing 1 barcoding 1 adapter 1 crispr-target 1 barcode 1 direct RNA sequencing 1 variants 1 long-read-sequencing 1 pacbio-ccs 1 genome-variation 1 assembly-polishing 1 time-series 1 signal-processing 1 data-analysis 1 single-molecule 1 timeseries 1 tensorflow 1 plant 1 qualitycontrol 1 plot 1 cli 1 bacteria 1 mycobacterium-tuberculosis 1 drug-resistance-prediction 1 resistance-prediction 1 diagnostics 1 tuberculosis 1 sam 1 ont 1 bam 1 fast5seek 1 robustness 1 low-biomass 1 lmat 1 kraken 1 contamination 1