Biopython | pypi | Package Usage

hungqcao/decision-tree-flu-prediction-excercise

==1.67 requirements.txt

Size: 305 KB - Last synced: over 1 year ago - Pushed: almost 2 years ago

ElofssonLab/ProQ4

* requirements.txt

Size: 27.6 MB - Last synced: about 2 months ago - Pushed: about 4 years ago

OluwadareLab/ParticleChromo3D_Plus

A Web-Server implementation of ParticleChromo3D for 3D chromosome structure reconstruction

==1.78 config/requirements.txt

Size: 2.99 MB - Last synced: 6 months ago - Pushed: 6 months ago

Ensembl/python-requirements

Sets of requirements files required to install a tool or setup a virtualenv

* tony_cwltool/requirements.txt

Size: 37.1 KB - Last synced: about 2 months ago - Pushed: about 1 year ago

PAiewsakun/GRAViTy

* setup.py

Size: 50.8 MB - Last synced: over 1 year ago - Pushed: about 2 years ago

szabgab/slides

The source of the slides of Gabor Szabo shared on the Code Maven site

* python/requirements.txt

Size: 14.6 MB - Last synced: about 1 month ago - Pushed: 4 months ago

phoenixding/tbsp

Trajectory Inference Based on SNP information.

>=1.72 setup.py

Size: 26.7 MB - Last synced: about 1 month ago - Pushed: over 2 years ago

xji3/IGCexpansion

IGC expansion code development folder

* requirements.txt
* setup.py

Size: 2.37 MB - Last synced: 4 months ago - Pushed: 4 months ago

YosefLab/Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

>=1.71 pyproject.toml

Size: 46.2 MB - Last synced: 28 days ago - Pushed: 29 days ago

DSC-ENSB/DRUGOC-project

DSC Solution Challenge - DRUGOC || Data files at https://github.com/Salem-Abderaouf/Drugoc-Data-files/

* DrugOC/Back-end/requirement.txt

Size: 63.1 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

GPCR-ModSim/qfepweb

Development of the web interface to QligFEP.

==1.78 requirements.txt

Size: 2.41 MB - Last synced: 8 months ago - Pushed: over 2 years ago

ni-sh-a-char/Bio.Informatica

A Common Platform for the study related to Bioinformatics, Computational Biology and Computational Chemistry.

* requirements.txt

Size: 25.2 MB - Last synced: 9 months ago - Pushed: 9 months ago

andrewguy/biostructmap

A Python package for mapping sequence aligned data onto protein structures

>=1.66 setup.py

Size: 1.16 MB - Last synced: about 1 month ago - Pushed: about 3 years ago

CFSAN-Biostatistics/snp-pipeline

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.

* setup.py

Size: 133 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

med-team/cutesv

comprehensive discovery of structural variations of genomic sequences

* setup.py

Last synced: about 1 year ago

univieCUBE/deepnog

Protein orthologous group assignment with deep learning

>=1.74 requirements/prod.txt
* setup.py

Size: 4.51 MB - Last synced: about 8 hours ago - Pushed: about 1 year ago

TUS-Satolab/PROP

==1.74 requests/requirements.txt

Size: 11 MB - Last synced: 2 months ago - Pushed: over 1 year ago

chunxiangli/Canopy

Iterative alignment and phylogeny inference tool with Prank and PAGAN

>=1.58 setup.py

Size: 37 MB - Last synced: about 1 year ago - Pushed: about 9 years ago

jorgedb98/SBI

* complex_assembler/setup.py

Size: 28.5 MB - Last synced: 10 months ago - Pushed: about 3 years ago

tobbeost/hirbin

hirbin repository

* setup.py

Size: 177 MB - Last synced: 6 months ago - Pushed: almost 8 years ago

hawaiidatascience/metaflowmics

C-MAIKI ITS and 16S pipelines

* metaflowmics/multithreaded-demux/py_requirements.txt

Size: 29.4 MB - Last synced: 2 months ago - Pushed: 2 months ago

HurlesGroupSanger/indelible

Structural Variation breakpoint discovery via adaptive learning

==1.74 requirements.txt

Size: 106 MB - Last synced: 8 months ago - Pushed: 11 months ago

alexholehouse/Geeneus

Simple base-type based API for the NCBI databases

* setup.py

Size: 1.33 MB - Last synced: 2 days ago - Pushed: almost 9 years ago

jimmyjamesarnold/annoPipeline

Uses mygene.info and Entrez APIs to annotate gene lists.

>=1.73 annoPipeline.egg-info/requires.txt
* setup.py

Size: 698 KB - Last synced: 2 days ago - Pushed: about 5 years ago

saketkc/riboraptor

Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)

>=1.70 requirements.txt

Size: 186 MB - Last synced: about 1 month ago - Pushed: over 3 years ago

nickp60/riboSeed

pipeline for using ribosomal flanking regions to improve bacterial genome assembly

==1.76 requirements.txt

Size: 492 MB - Last synced: 18 days ago - Pushed: almost 4 years ago

Edinburgh-Genome-Foundry/genome_collector

:stars: Easily download genomes and build BLAST/Bowtie indexes in Python

* setup.py

Size: 367 KB - Last synced: 24 days ago - Pushed: over 1 year ago

Edinburgh-Genome-Foundry/Geneblocks

:diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

* setup.py

Size: 1.48 MB - Last synced: 10 days ago - Pushed: almost 2 years ago

tonyyzy/GC_analysis

A command-line utility for calculating GC percentages of genome sequences

* requirements.txt
* setup.py

Size: 645 KB - Last synced: about 1 month ago - Pushed: over 5 years ago

MMichel/contact-vis

Python package for simple protein residue-residue contact map plotting.

* setup.py

Size: 962 KB - Last synced: 18 days ago - Pushed: over 9 years ago

bouralab/Prop3D

A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cleaned" domain structure in CATH.

* requirements.txt

Size: 265 MB - Last synced: 6 days ago - Pushed: 6 days ago

AMCeScience/PmedConnect

* setup.py

Size: 36.1 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago

oacar/enm_package

* requirements.txt

Size: 143 MB - Last synced: over 1 year ago - Pushed: almost 2 years ago

4dn-dcic/dcicwrangling

1.76 pyproject.toml

Size: 33.9 MB - Last synced: about 1 month ago - Pushed: 2 months ago

ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.

* setup.py

Size: 51.6 MB - Last synced: about 2 months ago - Pushed: over 1 year ago

Gab0/straintables

Compare genomic regions across organism strains.

>=1.73 requirements.txt

Size: 2.19 MB - Last synced: 4 days ago - Pushed: over 2 years ago

jakob-he/string-kernel

A python package that includes a variety of string kernel methods.

* setup.py

Size: 9.42 MB - Last synced: 4 days ago - Pushed: over 4 years ago

AstraZeneca/peptide-tools

Programs to calculate phys-chem properties of synthetic peptides and proteins: isoelectric point and extinction coefficients.

* requirements.txt

Size: 566 KB - Last synced: 8 days ago - Pushed: 9 days ago

pzelasko/daseg

Dialog Acts SEGmentation: Tools for dialog act research

* requirements.txt

Size: 2.47 MB - Last synced: 10 months ago - Pushed: about 2 years ago

edmundlth/primer_design

* setup.py

Size: 210 KB - Last synced: 3 months ago - Pushed: over 8 years ago

omixlab/bfscan

* requirements.txt

Size: 11.9 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

Edinburgh-Genome-Foundry/GoldenHinges

:link: Short overhangs design for DNA assembly

* setup.py

Size: 7 MB - Last synced: 2 months ago - Pushed: almost 2 years ago

sacgf/biographserv

Bio Graph Server generates visualisations for small biological data (bed, gene expression, VCF etc)

* requirements.txt

Size: 6.91 MB - Last synced: almost 2 years ago

Phelimb/metasort 📦

A Digital Health Hack Weekend Project using OneCodex API. Filter reads based on taxonomy assignment from OneCodex.

* requirements.txt

Size: 1.51 MB - Last synced: 3 months ago - Pushed: about 9 years ago

Pranavkhade/GOFindBias

The current main function of this project is to help people with .gaf file analysis.

* GOFindBias.egg-info/requires.txt
* setup.py

Size: 2.54 MB - Last synced: 3 days ago - Pushed: over 6 years ago

bouralab/DeepUrfold

Explore protein fold space with deep generative models

* requirements.txt

Size: 11 MB - Last synced: 5 days ago - Pushed: 6 days ago

nanoporetech/taiyaki 📦

Training models for basecalling Oxford Nanopore reads

* setup.py

Size: 53.5 MB - Last synced: 29 days ago - Pushed: over 2 years ago

Athemis/charm

CHarm provides codon harmonization for heterologous expression systems.

* requirements.txt

Size: 67.4 KB - Last synced: about 1 year ago - Pushed: over 6 years ago

NBCLab/nimare-paper

Code for NiMARE software paper

==1.78 binder/requirements.txt

Size: 192 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

simpsonlab/preqclr

preqclr is a software tool that reports on quality for long read sequencing data without the use of a reference genome.

* setup.py

Size: 13.2 MB - Last synced: about 1 month ago - Pushed: over 5 years ago

jmcarp/neurotrends

Identifying trends in neuroscience research.

==1.64 requirements.txt

Size: 6.14 MB - Last synced: 8 months ago - Pushed: over 9 years ago

Edinburgh-Genome-Foundry/DnaChisel

:pencil2: A versatile DNA sequence optimizer

* setup.py

Size: 9.2 MB - Last synced: 8 days ago - Pushed: about 1 year ago

Edinburgh-Genome-Foundry/DnaWeaver

A route planner for DNA assembly

* setup.py

Size: 3.98 MB - Last synced: about 1 month ago - Pushed: 8 months ago

mshakya/piret

Pythonic PiReT

==1.68 requirements.txt

Size: 393 MB - Last synced: 3 months ago - Pushed: 3 months ago

Edinburgh-Genome-Foundry/DnaCauldron

:alembic: Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies

* setup.py

Size: 3.41 MB - Last synced: 10 days ago - Pushed: 10 months ago

luo-chengwei/vargraph

varGraph: expand series metagenomics to variation graph analysis

>=1.66 setup.py
>=1.66 vargraph.egg-info/requires.txt

Size: 1.98 MB - Last synced: almost 2 years ago

ArmaanAhmed22/gRNA_create

Tool to design gRNAs

==1.79 requirements.txt

Size: 125 KB - Last synced: 4 days ago - Pushed: over 2 years ago

PawelSzczerbiak/cif2pdb

Convert mmCIF to PDB protein structure file format

* setup.py

Size: 4.19 MB - Last synced: 10 months ago - Pushed: about 1 year ago

mjnur/oomycete-effector-prediction

>=1.73 requirements.txt

Size: 29 MB - Last synced: 3 months ago - Pushed: 11 months ago

SBRG/ecolime

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

* setup.py

Size: 13.3 MB - Last synced: 9 days ago - Pushed: almost 5 years ago

RomainFeron/py_vectorbase_utils

Collection of utilities to use VectorBase in python3

* requirements.txt

Last synced: 26 days ago

ArthurVM/Afanc

Afanc high-resolution metagenomics disambiguator

==1.79 setup.py

Size: 198 MB - Last synced: 5 months ago - Pushed: 5 months ago

mattjones315/KPTracer-release

Code & utilities for the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"

* cassiopeia-kp/docs/requirements.txt

Size: 64.2 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

duocang/pipasic

pipasic - peptide intensity-weighted proteome abundance similarity correction

==1.76 requirements.txt
==1.76 setup.py

Size: 6.35 MB - Last synced: 8 months ago - Pushed: 11 months ago

sjspielman/pyvolve

Python library to simulate evolutionary sequence data

* setup.py

Size: 11 MB - Last synced: 15 days ago - Pushed: over 2 years ago

nickp60/pyutilsnrw

==1.68 requirements.txt
* setup.py

Size: 5.57 MB - Last synced: 8 days ago - Pushed: over 6 years ago

nickp60/happie

Horizontally Aquired Partial Pangenome of Inserted Elements

* requirements.txt
* setup.py

Size: 910 KB - Last synced: about 1 month ago - Pushed: about 4 years ago

tjiangHIT/rMETL

rMETL - realignment-based Mobile Element insertion detection Tool for Long read

* setup.py

Size: 1.02 MB - Last synced: about 1 month ago - Pushed: 10 months ago

raghu1991.p/daseg

Dialog Acts SEGmentation: Tools for dialog act research

* requirements.txt

Last synced: over 1 year ago

Phelimb/atlas

atlas

* requirements.txt
* setup.py

Size: 3.58 MB - Last synced: 9 days ago - Pushed: over 6 years ago

nickp60/EzClermont

Phylotype your strains using Clermont's 2013 method: ezclermont.org

* requirements.txt
* webapp/requirements.txt

Size: 81 MB - Last synced: 3 days ago - Pushed: almost 2 years ago

zachcp/qiime-tools

utilities for Qiime workflows

* setup.py

Size: 720 KB - Last synced: about 1 year ago - Pushed: almost 8 years ago

Mykrobe-tools/mykrobe

Antibiotic resistance prediction in minutes

>=1.79 requirements.txt
* setup.py

Size: 3.55 MB - Last synced: 15 days ago - Pushed: 16 days ago

Edinburgh-Genome-Foundry/easy_dna

:school_satchel: Python library to read, write, edit DNA sequences

* setup.py

Size: 322 KB - Last synced: 24 days ago - Pushed: over 1 year ago

Amine-Namouchi/snpToolkit

* setup.py

Size: 13.9 MB - Last synced: 17 days ago - Pushed: about 3 years ago

FriedbergLab/GOThresher

* gothresher.egg-info/requires.txt
* setup.py

Size: 34.1 MB - Last synced: 22 days ago - Pushed: about 2 months ago

kblin/skeleton

* requirements.txt

Size: 4.95 MB - Last synced: almost 2 years ago

yuvipanda/mybinder.org-analytics 📦

Notebooks & code for analyzing mybinder.org statistics

* sparse/repos/CropEvol/remote_py3/requirements.txt

Size: 4.14 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago

evogenlab/py_vectorbase_utils

Collection of utilities to use VectorBase in python

* requirements.txt

Last synced: over 1 year ago

BIMSBbioinfo/janggu

Deep learning infrastructure for genomics

==1.77 setup.py

Size: 6.33 MB - Last synced: 4 months ago - Pushed: over 2 years ago

compbiomed-unito/acdc-nn

>=1.78 setup.py

Size: 38.3 MB - Last synced: 21 days ago - Pushed: over 1 year ago

RubyvanderHolst/interface-dnabarcoder

An interface of dnabarcoder (https://github.com/vuthuyduong/dnabarcoder)

* requirements.txt

Size: 2.53 MB - Last synced: 8 months ago - Pushed: 8 months ago

baijuyi/pipasic

==1.76 requirements.txt
==1.76 setup.py

Last synced: about 9 hours ago

EMSL-Computing/grip-tomo

docs: https://grip-tomo.readthedocs.io/en/latest/

==1.78 requirements.txt

Size: 967 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

clauswilke/codon_tools

A python package containing various tools for codon optimization and de-optimization.

* setup.py

Size: 46.9 KB - Last synced: 29 days ago - Pushed: about 7 years ago

neilswainston/CodonGenie

CodonGenie

* requirements.txt

Size: 1.68 MB - Last synced: 18 days ago - Pushed: over 1 year ago

Package Usage: pypi: Biopython

Dependent Repos 101

Phelimb/metasort 📦

nanoporetech/taiyaki 📦

yuvipanda/mybinder.org-analytics 📦