Reverse Dependencies of biopython
The following projects have a declared dependency on biopython:
- snipit — snipit
- snpio — Reads and writes VCF, PHYLIP, and STRUCTURE files and performs data filtering on the alignment.
- snpToolkit — SNPs filtering, annotation and combining
- socialgene — Creating and interacting with graph databases of protein domains and their genome coordinates
- sphae — Assembling pure culture phages from both Illumina and Nanopore sequencing technology
- spora — spora: Streamlined Phylogenomic Outbreak Report Analysis
- spyProt — This package provides a set of tools for accessing protein databases and manipulating PDB/CIF files.
- sramongo — A package to download metadata from SRA/Biosample/Geo and dump into a mongo database.
- srapy — SRApy: Scripts to download SRA files
- SRRec — Short Reads Rectification
- ssbio-edbr — Tools to enable structural systems biology, forked from SBRG/ssbio
- ssbtoolkit — Simulation of methematical models of signaling pathways of GPCRs
- ssrviz — Protein subfamily specific residue (SSR) detection and visualization toolbox
- STAPAMRTime — Metagenomic AMR variant detection tool, part of ARMTime.
- staramr — Scans genome contigs against ResFinder, PlasmidFinder, and PointFinder databases
- stepRNA — Align short RNA seqeuncing reads to determine the length of of overhang.
- stepwise_mol_bio — Protocols relating to molecular biology, e.g. PCR.
- STFD — STFD: Series of deep learning-based foundation models for spatial transcriptomic data analysis
- stranding — Determine genome stranding for sequences mapped to a human reference assembly
- strkernel — Collection of string kernels
- Structuralia — A toolset to work with proteins
- subhelper — Helper scripts for submission to ena (microbial + sarscov2) and gisaid (sarscov2 only)
- subsample-fastas — Randomly alter fasta files by substracting a given % of genes in a genome (fasta) or in a (% of a) set of genomes
- sumonet — Package Description
- superseal — Reference-guided viral quasipsecies reconstruction
- sweep — SWeeP is a tool for representing large biological sequences datasets in compact vectors
- synbio — Synbio design and build library
- synbiochem-py — synbiochem-py: Core python modules for SYNBIOCHEM
- synbiopython — Python tools for Synthetic Biology.
- synphage — Python library for plotting synteny diagram for phage and bacterial sequences.
- synthaser — Automatic prediction and classification of protein domain architectures
- synthego-ice — Synthego - Inference of CRISPR Edits (ICE)
- T4SEfinder — A bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model.
- tacape — TACaPe: Transformed-based Anti-Cancer Peptide Classification and Generation
- tacl — Text analyser for corpus linguistics
- tadrep — TaDRep: Targeted Detection and Reconstruction of Plasmids
- taiga-bio — Set of tools to fetch taxonomic metadata for a list of organisms
- tape-proteins — Repostory of Protein Benchmarking and Modeling
- tax2peptide — tax2peptide creates based on given taxon IDs and a reference database a taxon specific database in fasta format.
- tax2proteome — tax2proteome creates based on given taxon IDs and a reference database a taxon specific database in fasta format.
- taxmyphage — Script to assign taxonomy to a bacteriophage at the genus and species level
- taxoniumtools — Generate files for taxonium
- taxonize-gb — Python package to download and filter GenBank database based on taxonomy
- taxontabletools — TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data
- tbsp — SNP-based trajectory inference
- teemi — A Python package for constructing microbial strains
- teritori — Replications origin and terminus prediction in bacterial genomes
- tessellate — A package for quantifying cyclic molecule conformations.
- textdiversity — A family of textual diversity metrics
- tf-bind-transformer — Transformer for Transcription Factor Binding
- TFBS-footprinting — Tool for identifying conserved TFBSs in vertebrate species.
- TFBS-footprinting3 — Tool for identifying conserved TFBSs in vertebrate species.
- thapbi-pict — THAPBI Phytophthora ITS1 Classifier Tool (PICT).
- thoipapy — Machine-learning prediction of residues driving homotypic transmembrane interactions.
- thoraxe — Disentangle homology relationships between exons.
- threed-strudel — Strudel package
- tictax — Streaming nucleotide sequence classification with web services
- TIdeS-ML — Tool for ORF-calling and ORF-classification using ML approaches
- TileSeqMut — Analysis scriptsTileSeqMut for TileSeq sequencing data
- tiptoft — tiptoft: predict which plasmid should be present from uncorrected long read data
- ToolBiox — a biological toolkit for genome assembly, annotation and analysis that we have accumulated from our bioinformatics work
- topoly — This package provides a set of tools for modeling protein knots, lassos and other.
- torchcell — An example package
- torchmetagen — Torchmetagen is a python package for metagenomic sequence data processing and inference.
- track-duplicates — A simple tool to extract reads from a certain taxa from BAM files
- trackcluster — RNA-seq analysis for Long read RNA sequencing
- trails-rivasiker — Tree reconstruction of ancestry using incomplete lineage sorting
- tral — Detect and evaluate tandem repeats in genomic sequence data.
- transport-tools — a library for massive analyses of internal voids in biomolecules and ligand transport through them
- treasureisland — Prediction of Genomic Islands
- treeCl — Phylogenetic Clustering Package
- TreeSAK — BioSAK
- trialhub — Helper modules for TrialHub project
- trialhub-helpers — Helper modules for TrialHub project
- trifl — TRIFL is a data filtration library for MS-proteomics experiments.
- trisicell — Trisicell - Scalable tumor phylogeny reconstruction and validation from single-cell data
- Troika-TB — A pipeline implementing TB-Profiler for batch detection and reporting of anti-microbial resistance in TB for public health and clinical use.
- trviz — A python library for decomposing and visualizing tandem repeat sequences
- unassigner — Bacterial species unassigner
- uniprotpy — A Python library that interfaces with UniProt data.
- uniqmin — An alignment-independent tool for the study of pathogen sequence diversity at any given rank of taxonomy lineage
- uorf4u — A tool for short uORF annotation.
- urban_metagenomics_tutorial — Metagenomics utilities
- usum — USUM: Plotting sequence similarity using USEARCH & UMAP
- UTRme — UTRme
- VA — CryoEM validation toolkit
- varcode — Variant annotation in Python
- varconv — no summary
- variamotif — A Computational Tool for Variable Motif scanning and Sequence-based Relative Position Visualization of Search Results in Sequences.
- variantworks — NVIDIA genomics python libraries and utiliites
- varvamp — Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses
- vaxpress — Codon Optimizer for mRNA Vaccine Design
- vcf-consensus-builder — Build a consensus sequence from a VCF and ref sequence masking low and no coverage positions.
- VCF-kit — Assorted utilities for the variant call format
- vcfio — A simple and efficient VCF manipulation package.
- vcfsynonymous — Detect synonymous genetic variants in VCF
- vcftoolz — Tools for working with Variant Call Format files.
- vcfy — Generate VCF file with random variants from reference genome
- vclean — vClean: Assessing the contamination of viral genomes
- vegvisir — Vegvisir