dnbc4dev 2.3.9

DNBelab Series Single-Cell analysis workflow
37 versions - Latest release: 10 months ago - 1 dependent repositories - 277 downloads last month - 50 stars on GitHub - 1 maintainer

rohittools 0.1.1

Analysis of single-cell Massively Parallel Reporter Assay (MPRA) data
2 versions - Latest release: 10 months ago - 77 downloads last month - 1 maintainer

str-analysis 1.2.10

Utilities for analyzing short tandem repeats (STRs)
43 versions - Latest release: 10 months ago - 1 dependent repositories - 1.03 thousand downloads last month - 36 stars on GitHub - 1 maintainer

polygenic 2.3.17

Polygenic score toolkit
124 versions - Latest release: 10 months ago - 1 dependent repositories - 4.06 thousand downloads last month - 0 stars on GitHub - 1 maintainer

mdeepfri 1.1.8

Pipeline for searching and aligning contact maps for proteins, and function prediction with DeepFRI.
8 versions - Latest release: 10 months ago - 1.24 thousand downloads last month - 37 stars on GitHub - 1 maintainer

Top 5.2% on pypi.org

checkm-genome 1.2.3

Assess the quality of putative genome bins.
40 versions - Latest release: 10 months ago - 1 dependent package - 8 dependent repositories - 2.31 thousand downloads last month - 318 stars on GitHub - 1 maintainer

pattools-methy 0.1.0

pattools is a BS-seq analysis tool suite based on pat format
1 version - Latest release: 10 months ago - 45 downloads last month - 2 stars on GitHub - 1 maintainer

yasim 3.2.1

Yet Another SIMulator for Alternative Splicing Events and Realistic Gene Expression Profile
3 versions - Latest release: 10 months ago - 1 dependent package - 129 downloads last month - 1 stars on GitHub - 1 maintainer

biometrics 0.2.15

Package to generate sample based biometrics.
18 versions - Latest release: 10 months ago - 2 dependent repositories - 449 downloads last month - 4 stars on GitHub - 1 maintainer

brie 2.3.0

BRIE: Bayesian regression for isoform estimate
22 versions - Latest release: 10 months ago - 2 dependent repositories - 450 downloads last month - 7 stars on GitHub - 1 maintainer

fuc 0.38.0 💰

Frequently used commands in bioinformatics
39 versions - Latest release: 10 months ago - 1 dependent package - 2 dependent repositories - 3.23 thousand downloads last month - 48 stars on GitHub - 1 maintainer

labw-utils 1.0.4

Utilities Python functions & classes used in LabW
3 versions - Latest release: 10 months ago - 2 dependent packages - 160 downloads last month - 0 stars on GitHub - 1 maintainer

tbpore 0.7.1

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
12 versions - Latest release: 11 months ago - 1 dependent repositories - 181 downloads last month - 11 stars on GitHub - 1 maintainer

sequenoscope 0.0.5

Description
1 version - Latest release: 11 months ago - 31 downloads last month - 5 stars on GitHub - 1 maintainer

imputehifi 0.1.3

3 versions - Latest release: 11 months ago - 70 downloads last month - 1 maintainer

bwalign 1.7.0

A burrows-wheeler seed and extend aligner
24 versions - Latest release: 11 months ago - 457 downloads last month - 0 stars on GitHub - 1 maintainer

hellobc 0.1.0

XuLab package for single-cell RNA-seq data upstream processing.
1 version - Latest release: 11 months ago - 42 downloads last month - 1 maintainer

dispbind 1.1.0

Disorder protein genomic binding analysis toolkit
3 versions - Latest release: 11 months ago - 135 downloads last month - 6 stars on GitHub - 1 maintainer

smallgenomeutilities 0.4.1

A collection of scripts that are useful for dealing with viral RNA NGS data.
6 versions - Latest release: 11 months ago - 1 dependent repositories - 158 downloads last month - 11 stars on GitHub - 3 maintainers

Top 9.7% on pypi.org

sinto 0.10.1

Tools for single-cell data processing
33 versions - Latest release: 11 months ago - 3 dependent repositories - 746 downloads last month - 123 stars on GitHub - 1 maintainer

phlash 1.0.3

Bayesian inference of population size history from recombining sequence data.
4 versions - Latest release: 11 months ago - 162 downloads last month - 7 stars on GitHub - 1 maintainer

gene4mvcf 1.1.5

Description of your package
5 versions - Latest release: 11 months ago - 121 downloads last month - 0 stars on GitHub - 1 maintainer

rlpipes 0.9.4

A standardized R-loop-mapping pipeline
5 versions - Latest release: 11 months ago - 1 dependent repositories - 150 downloads last month - 3 stars on GitHub - 1 maintainer

metaphlan 4.1.1

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteri...
26 versions - Latest release: 11 months ago - 1 dependent repositories - 1.19 thousand downloads last month - 273 stars on GitHub - 2 maintainers

Top 8.3% on pypi.org

toolbiox 0.0.46

a biological toolkit for genome assembly, annotation and analysis that we have accumulated from o...
30 versions - Latest release: 11 months ago - 8 dependent packages - 2 dependent repositories - 1.1 thousand downloads last month - 1 maintainer

affipred 0.1.2

AlphaFold based Functional Impact Prediction of Missense Variations
5 versions - Latest release: 11 months ago - 170 downloads last month - 1 maintainer

bioh2m 1.0.3

For precision modeling of human variants in the mouse genome.
4 versions - Latest release: 11 months ago - 143 downloads last month - 0 stars on GitHub - 1 maintainer

cvmtrans 0.0.9

Transposon data process
5 versions - Latest release: 12 months ago - 153 downloads last month - 0 stars on GitHub - 1 maintainer

lhc-python 2.5.1

My personal package for bioinformatics related stuff
37 versions - Latest release: 12 months ago - 3 dependent repositories - 820 downloads last month - 0 stars on GitHub - 1 maintainer

wgscovplot 1.0.2

Create interactive comparative sequencing coverage plots from virus sequencing data.
8 versions - Latest release: 12 months ago - 1 dependent repositories - 212 downloads last month - 19 stars on GitHub - 2 maintainers

spectre-cnv 0.2.1

Long read copy number variation (CNV) caller
2 versions - Latest release: 12 months ago - 103 downloads last month - 58 stars on GitHub - 1 maintainer

dnbc4tools 2.1.2

DNBelab Series Single-Cell analysis workflow
19 versions - Latest release: 12 months ago - 1 dependent repositories - 489 downloads last month - 50 stars on GitHub - 1 maintainer

scallele 0.0.9.4

A versatile tool for the detection and analysis of nucleotide variants in scRNA-seq
3 versions - Latest release: about 1 year ago - 156 downloads last month - 23 stars on GitHub - 1 maintainer

ehdnexact 0.1.1

Refines approximate repeat regions identified by ExpansionHunter denovo to exact genomic coordinates
2 versions - Latest release: about 1 year ago - 43 downloads last month - 0 stars on GitHub - 1 maintainer

ribotricer 1.4.0

Python package to detect translating ORFs from Ribo-seq data
10 versions - Latest release: about 1 year ago - 1 dependent repositories - 218 downloads last month - 31 stars on GitHub - 1 maintainer

Top 6.5% on pypi.org

cnvkit 0.9.11

Copy number variation toolkit for high-throughput sequencing.
50 versions - Latest release: about 1 year ago - 2 dependent repositories - 2.56 thousand downloads last month - 1 maintainer

panisa 0.1.7

panISa is a software to search insertion sequence (IS) on resequencing data (bam file)
9 versions - Latest release: about 1 year ago - 1 dependent repositories - 288 downloads last month - 22 stars on GitHub - 1 maintainer

genomkit 0.2.8

genomkit
6 versions - Latest release: about 1 year ago - 119 downloads last month - 0 stars on GitHub - 1 maintainer

modbedtools 0.1.6

Generate modbed track files for visualization on WashU Epigenome Browser
7 versions - Latest release: about 1 year ago - 150 downloads last month - 9 stars on GitHub - 1 maintainer

cnvoyant 1.1.6

Copy Number Variant Pathogenicity Classifier
62 versions - Latest release: about 1 year ago - 1.17 thousand downloads last month - 1 stars on GitHub - 1 maintainer

miraclepy 0.1

Microsatellite Instability (MSI) detection with RNA sequencing data.
1 version - Latest release: about 1 year ago - 45 downloads last month - 0 stars on GitHub - 1 maintainer

uta-align 0.3.0

C-based sequence alignment for Python
21 versions - Latest release: about 1 year ago - 3 dependent repositories - 1.43 thousand downloads last month - 5 stars on GitHub - 4 maintainers

ilmn-pelops 0.8.0

Dedicated caller for DUX4 rearrangements from whole genome sequencing data.
3 versions - Latest release: about 1 year ago - 134 downloads last month - 3 stars on GitHub - 2 maintainers

maskara 1.0.0

maskara
1 version - Latest release: about 1 year ago - 55 downloads last month - 1 stars on GitHub - 1 maintainer

align-trim2 1.0.0

2 versions - Latest release: about 1 year ago - 100 downloads last month - 1 maintainer

plassembler 1.6.2

Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates
10 versions - Latest release: about 1 year ago - 260 downloads last month - 60 stars on GitHub - 1 maintainer

cutefc 1.0.0

Regenotyping structural variants through an accurate and efficient force-calling method
1 version - Latest release: about 1 year ago - 78 downloads last month - 0 stars on GitHub - 1 maintainer

demuxalot 0.4.1

Scalable and reliable demulitplexing for single-cell RNA sequencing.
2 versions - Latest release: about 1 year ago - 1 dependent repositories - 146 downloads last month - 24 stars on GitHub - 1 maintainer

cobra-meta 1.2.3

COBRA (Contig Overlap Based Re-Assembly) is a bioinformatics tool to get higher quality viral gen...
4 versions - Latest release: about 1 year ago - 180 downloads last month - 43 stars on GitHub - 1 maintainer

Top 8.7% on pypi.org

insilicoseq 2.0.1

a sequencing simulator
39 versions - Latest release: about 1 year ago - 4 dependent repositories - 646 downloads last month - 172 stars on GitHub - 1 maintainer

ezancestry 0.1.0

Easily predict and visualize genetic ancestry. Evaluate custom ancestry-informative SNP sets.
8 versions - Latest release: about 1 year ago - 1 dependent package - 1 dependent repositories - 478 downloads last month - 65 stars on GitHub - 1 maintainer

ngs-chew 0.9.4

NGS Chew
11 versions - Latest release: about 1 year ago - 200 downloads last month - 3 stars on GitHub - 1 maintainer

circulocov 0.1.20240104

Circular-Aware Coverage for Draft Genomes
1 version - Latest release: about 1 year ago - 60 downloads last month - 7 stars on GitHub - 1 maintainer

yap-gcp 1.7.8

Pipelines for single nucleus methylome and multi-omic dataset.
1 version - Latest release: about 1 year ago - 14 stars on GitHub - 1 maintainer

beditor 2.0.1

A computational workflow for designing libraries of guide RNAs for CRISPR base editing
20 versions - Latest release: about 1 year ago - 1 dependent repositories - 91 downloads last month - 19 stars on GitHub - 1 maintainer

mates 0.1.4

4 versions - Latest release: about 1 year ago - 83 downloads last month - 1 maintainer

splicekit 0.5.1

splicekit: comprehensive toolkit for splicing analysis from short-read RNA-seq
14 versions - Latest release: about 1 year ago - 279 downloads last month - 16 stars on GitHub - 1 maintainer

vcfio 1.1.9

A simple and efficient VCF manipulation package.
11 versions - Latest release: about 1 year ago - 1 dependent repositories - 857 downloads last month - 6 stars on GitHub - 1 maintainer

corecomb 0.2.1

Toolkit to deal with core-genome alignments recombination detection
3 versions - Latest release: about 1 year ago - 134 downloads last month - 1 stars on GitHub - 1 maintainer

culebront 3.0.0

CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch m...
8 versions - Latest release: about 1 year ago - 1 dependent repositories - 214 downloads last month - 0 stars on GitHub - 3 maintainers

motifdiff 0.1 removed

1 version - Latest release: about 1 year ago - 1 maintainer

Top 5.2% on pypi.org

ephemeris 0.10.10

Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy p...
24 versions - Latest release: about 1 year ago - 1 dependent package - 43 dependent repositories - 9.5 thousand downloads last month - 27 stars on GitHub - 4 maintainers

sma-finder 1.4.4

A tool for diagnosing spinal muscular atrophy (SMA) using exome or genome sequencing data
11 versions - Latest release: about 1 year ago - 638 downloads last month - 11 stars on GitHub - 1 maintainer

cpat 3.0.5

CPAT (Coding Potential Assessment Tool).
7 versions - Latest release: about 1 year ago - 426 downloads last month - 11 stars on GitHub - 1 maintainer

psite 0.1.6

Model-based inference of P-site offsets
5 versions - Latest release: about 1 year ago - 186 downloads last month - 3 stars on GitHub - 1 maintainer

indelpost 0.2.3

Python library for simple and complex indels
20 versions - Latest release: about 1 year ago - 2 dependent packages - 1 dependent repositories - 632 downloads last month - 13 stars on GitHub - 1 maintainer

bam2tensor 1.0.1

Bam2Tensor
10 versions - Latest release: over 1 year ago - 342 downloads last month - 1 stars on GitHub - 1 maintainer

amplicon-coverage-inspector 1.4.20240116

Visualization of coverage for amplicon sequencing
3 versions - Latest release: over 1 year ago - 127 downloads last month - 3 stars on GitHub - 1 maintainer

mgatk 0.7.0

Mitochondrial genome analysis toolkit.
21 versions - Latest release: over 1 year ago - 1 dependent repositories - 501 downloads last month - 90 stars on GitHub - 1 maintainer

fast5_rekindler 0.0.6

Collates information from BAM and POD5 files and generates FAST5 files for use in legacy tools su...
5 versions - Latest release: over 1 year ago - 136 downloads last month - 1 stars on GitHub - 1 maintainer

schickit 0.0.59

a toolkit for processing single cell Hi-C data
55 versions - Latest release: over 1 year ago - 1.7 thousand downloads last month - 1 maintainer

Top 4.7% on pypi.org

vcfpy 0.13.8

Python 3 VCF library with good support for both reading and writing
27 versions - Latest release: over 1 year ago - 14 dependent packages - 37 dependent repositories - 11.2 thousand downloads last month - 78 stars on GitHub - 1 maintainer

mclumi 0.0.4

UMI de-duplication using mclUMI
3 versions - Latest release: over 1 year ago - 143 downloads last month - 1 stars on GitHub - 1 maintainer

mutview 0.0.1

A command tool to view reads over a loci from bam file, like a lightweigth IGV
1 version - Latest release: over 1 year ago - 45 downloads last month - 13 stars on GitHub - 1 maintainer

scdna-replication-tools 0.0.1

Code for analyzing single-cell replication dynamics
1 version - Latest release: over 1 year ago - 50 downloads last month - 1 stars on GitHub - 1 maintainer

funnsv 0.0.2

Fast and effective functional annotation of SVs
2 versions - Latest release: over 1 year ago - 127 downloads last month - 0 stars on GitHub - 1 maintainer

insilicosv 0.0.6

Simulator of complex structural variants in genomes
3 versions - Latest release: over 1 year ago - 130 downloads last month - 11 stars on GitHub - 1 maintainer

sam2lca 1.1.4

Lowest Common Ancestor on SAM/BAM/CRAM alignment files
14 versions - Latest release: over 1 year ago - 1 dependent repositories - 500 downloads last month - 9 stars on GitHub - 1 maintainer

atropos 1.1.32

trim adapters from high-throughput sequencing reads
62 versions - Latest release: over 1 year ago - 3 dependent repositories - 1.59 thousand downloads last month - 121 stars on GitHub - 1 maintainer

angua-luggage 0.1.8

16 versions - Latest release: over 1 year ago - 444 downloads last month - 1 maintainer

xlavir 1.0.2

Excel report from viral sequencing analysis output
21 versions - Latest release: over 1 year ago - 1 dependent repositories - 728 downloads last month - 3 stars on GitHub - 1 maintainer

midas2 1.1.3

https://midas2.readthedocs.io/en/latest/
16 versions - Latest release: over 1 year ago - 1 dependent repositories - 520 downloads last month - 37 stars on GitHub - 1 maintainer

govcf 0.9.0

govcf
2 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 109 downloads last month - 70 stars on GitHub - 3 maintainers

varconv 0.1.2

3 versions - Latest release: over 1 year ago - 140 downloads last month - 1 maintainer

hisv 1.0.9

A computational pipeline for structural variation detection from Hi-C data
4 versions - Latest release: over 1 year ago - 148 downloads last month - 15 stars on GitHub - 1 maintainer

isocirc 1.0.7

isoCirc: computational pipeline to identify high-confidence BSJs and full-length circRNA isoforms...
8 versions - Latest release: over 1 year ago - 1 dependent repositories - 232 downloads last month - 10 stars on GitHub - 1 maintainer

mimseq 1.3.8

Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modificatio...
62 versions - Latest release: over 1 year ago - 1 dependent repositories - 1.75 thousand downloads last month - 21 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: over 1 year ago - 161 downloads last month - 1 stars on GitHub - 1 maintainer

reallyrun 0.1

Not your grandmas NGS analysis - software for analyzing FASTQs from REALLY libraries
1 version - Latest release: over 1 year ago - 52 downloads last month - 0 stars on GitHub - 1 maintainer

mutacc 1.7.2

The mutation accumulation database
5 versions - Latest release: over 1 year ago - 1 dependent repositories - 150 downloads last month - 2 stars on GitHub - 4 maintainers

maxatac 1.0.6

maxATAC: a suite of user-friendly, deep neural network models for transcription factor binding pr...
4 versions - Latest release: over 1 year ago - 1 dependent repositories - 114 downloads last month - 28 stars on GitHub - 1 maintainer

ciriquant 1.1.3

circular RNA quantification pipeline
7 versions - Latest release: over 1 year ago - 2 dependent repositories - 218 downloads last month - 28 stars on GitHub - 1 maintainer

triplix 0.0.5

A python package to efficiently process, store and retrieve spatial genomics multi-contact data
5 versions - Latest release: over 1 year ago - 169 downloads last month - 0 stars on GitHub - 1 maintainer

methylbert-hanyangii 0.0.1 removed

A Transformer-based model for read-level DNA methylation pattern identification and tumour deconv...
1 version - Latest release: over 1 year ago - 1 maintainer

strainge 1.3.9

Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains.
21 versions - Latest release: over 1 year ago - 2.88 thousand downloads last month - 7,299 stars on GitHub - 1 maintainer

eva-vcf-merge 0.0.8

EBI EVA - VCF merge library
9 versions - Latest release: over 1 year ago - 3 dependent repositories - 318 downloads last month - 0 stars on GitHub - 1 maintainer

cyrius 1.1.1

WGS-based CYP2D6 caller
1 version - Latest release: over 1 year ago - 67 downloads last month - 51 stars on GitHub - 1 maintainer

gauchian 1.0.2

WGS-based GBA variant caller
1 version - Latest release: over 1 year ago - 48 downloads last month - 21 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: over 1 year ago - 1 dependent repositories - 498 downloads last month - 11 stars on GitHub - 1 maintainer

handygenome 0.4.6

An integrated platform for genome sequencing analysis
7 versions - Latest release: over 1 year ago - 351 downloads last month - 1 stars on GitHub - 1 maintainer

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