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biopython

Here are 143 public repositories matching this topic...

biopython / biopython

Open

Define SeqFeature sub for integer offset

peterjc commented Jan 1, 2022

See https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py and __add__, need to do the same specifically for integer offsets.

Workaround feature + (-5) instead of feature - 5, see https://twitter.com/tomeraltman/status/1473764959347638273

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Enhancement good first issue

Open

silence warnings PDBConstructionWarning in test_PDB_StructureAlignment.py

4

Open

PAML run method docstrings - return value

16

Find more good first issues

dash-cytoscape

plotly / dash-cytoscape

Sponsor

Open

[Feature Request] expand/collapse of nodes

6

aloktiagi commented Aug 3, 2020

Hi,

It would be nice to have the capability to expand/collapse nodes similar to https://github.com/iVis-at-Bilkent/cytoscape.js-expand-collapse.

Thanks.

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good first issue suggestion

Open

Dash Cytoscape: control the scroll wheel sensitivity for zooming

7

Open

Improve interactions tests

1

modernatx / seqlike

Unified biological sequence manipulation in Python

machine-learning biopython sequence biological-sequences

Updated Apr 12, 2022
Python

pydna

BjornFJohansson / pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

python bioinformatics jupyter anaconda simulation biology jupyter-notebook dna biopython genbank gel fasta jupyter-notebooks anaconda-server-badge pydna gel-simulation gibson-assembly cloning-strategies gel-electrophoresis assembly-strategies

Updated Mar 31, 2022
Jupyter Notebook

ponnhide / pyCircos

Sponsor

python Circos

visualization python phylogenetic-trees biopython matplotlib circos circos-plot

Updated Apr 10, 2022
Jupyter Notebook

biopython-coronavirus

chris-rands / biopython-coronavirus

Biopython Jupyter Notebook tutorial to characterize a small genome

python bioinformatics genomics jupyter-notebook biopython coronavirus covid-19

Updated Apr 8, 2020
Jupyter Notebook

Zsailer / phylopandas

Pandas DataFrames for phylogenetics

python pandas biopython phylogenetics

Updated Jun 6, 2021
Python

RK900 / Flu-Prediction

Predicting Future Influenza Virus Sequences with Machine Learning

python machine-learning scikit-learn dna biopython flu-prediction flu

Updated Feb 11, 2018
Python

pyladies-brazil / grupo-estudo-bioinformatica

Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.

bioinformatics bioinformatics-pipeline biopython bioinformatics-analysis rosalind estudo

Updated Oct 10, 2021
Jupyter Notebook

RKMlab / perf

PERF is an Exhaustive Repeat Finder

genomics genome simple repeats ssr biopython fasta sequence tandem microsatellites

Updated Apr 22, 2021
HTML

widdowquinn / 2018-03-06-ibioic

Teaching materials for 6-7th March 2018 delivery of introductory bioinformatics training course for IBioIC.

python bioinformatics jupyter-notebook teaching biopython blast uniprot teaching-materials

Updated Mar 12, 2018
HTML

biosustain / goodbye-genbank

A Python package for Biopython that gives feature annotations from GenBank records a new and better life

genomics gff3 biopython genbank sequence-ontology

Updated Apr 27, 2016
Python

nalomran / pubmed2doc

Write PubMed search results with two display options (citation or listview) to PDF or Word

bioinformatics python3 pubmed pubmed-parser biopython docx fpdf

Updated Oct 18, 2020
Python

Protein-feature-extraction

jithin8mathew / Protein-feature-extraction

Python code to extract features from Protein sequences for Machine Learning/Deep Learning

windows linux machine-learning bioinformatics deep-learning bioinformatics-pipeline feature-extraction biopython protein-sequences fasta bioinformatics-data extract-features bioinformatics-analysis protein-feature-extraction

Updated Mar 26, 2022
Python

vinisalazar / BioProv

A provenance library for bioinformatics workflows 🧬

🔀

📝

python provenance biopython prov biological-data w3c-prov

Updated Oct 5, 2021
Python

dewshr / NCBI-GenBank-file-parser

This program can be used to parse the NCBI GenBank file to create a tabulated csv file.

python metadata parser extract-information biopython ncbi-genbank extract-data file-parser reference-data

Updated Mar 4, 2019
Python

bott0m / Needleman-Wunsch-Algorithm

Needleman-Wunsch Algorithm for global alignment and local alignment

algorithm dna protein biopython global-alignment sequences local-alignment neeldman-wunsch

Updated Feb 12, 2020
Python

althonos / moclo

Modular cloning simulation with the MoClo framework in Python

bioinformatics biopython plasmids system-biology modular-cloning moclo

Updated Nov 8, 2021
Python

rodogi / biographs

Python class to easily deal with protein networks.

protein-structure biopython amino-acid-network protein-contact-network

Updated May 23, 2020
Python

Edinburgh-Genome-Foundry / SnapGeneReader

👓 Python library to parse Snapgene *.dna files to dict or biopython seqrecord.

converter synthetic-biology biopython genbank sequence-design snapgene

Updated Sep 20, 2020
Python

laelbarlow / amoebae

Workflow for identifying and classifying homologous gene/protein sequences

bioinformatics python3 biopython gene-families genome-annotation blast comparative-genomics molecular-evolution similarity-search protein-families orthology homology snakemake-workflow hmmer3 transcriptome-annotation coulson-plot

Updated Mar 16, 2022
Python

kirai / bio_hacking

Biotech with biopython

biopython biotechnology

Updated Aug 2, 2017
Python

moshi4 / GBKviz

Easy-to-use web application for visualization and comparison of genomes in Genbank file using Streamlit, GenomeDiagram, MUMmer

visualization python bioinformatics genomics webapp biopython genbank microbial-genomics comparative-genomics genomics-visualization streamlit

Updated Apr 1, 2022
Python

cgoliver / RNA-Popgen-Notebook

Jupyter notebook for RNA evolutionary algorithm and subsequent population genetics and BioPython tools.

jupyter-notebook biopython rna population-genetics rna-evolutionary-algorithm

Updated Jun 14, 2016
Jupyter Notebook

MountainMan12 / SARS-Cov2-phylo

Analysis of the viral genomes of SARS-CoV2 using MAFFT and igtree

phylogenetic-trees biopython ncbi-database multiple-sequence-alignment

Updated Aug 14, 2020
Python

rob-miller / rFold

a set of classes and submodules to build, manipulate and analyse three-dimensional protein structures.

bioinformatics lua protein-structure luajit biopython 3d-printing dihedral-angles bioinformatics-tool residue-environments

Updated Sep 10, 2019
Python

yachielab / QUEEN

QUEEN: a framework to generate quinable and efficiently editable nucleotide sequence resources

bioinformatics biopython jupyter-notebooks plasmids

Updated Apr 11, 2022
Python

dillondaudert / proteindatasets

Creating and manipulating various protein sequence-structure datasets using Python, Julia, and other tools.

bioinformatics jupyter tensorflow julia structure jupyter-notebook pandas python3 dataset protein biopython fasta blast dssp secondary psiblast uniref50

Updated Sep 1, 2018
Jupyter Notebook

lorenzoFabbri / academic-networks

Small Python library to find possible supervisors and/or collaborators based on user-defined query (e.g., topics of interest) or user-defined author.

python networking pubmed biopython folium collaborators academia geopy geolocalization geotext

Updated May 2, 2020
HTML

althonos / orthoani

A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.

python bioinformatics biopython python-module average-nucleotide-identity orthoani

Updated May 28, 2021
Python

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