Reverse Dependencies of bio

The following projects have a declared dependency on bio:

• aphylogeo — A phylogenetic and geographic analysis tool
• arctic3d — Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
• ASVmaker — ASVmaker: A new tool to improve taxonomic identifications for amplicon sequencing data
• Augusta — Python package for inference of the gene regulatory network and the boolean network using RNA-Seq data.
• autocv — autoCV: An automated CV generator
• BIOecmpy — Automated construction of enzyme constraint models using ECMpy workflow
• biofile — Process various file format for RNA-Seq data analysis
• bioomics — Download, retrieve and process omics data for further bioinformatics
• biosequtils — Provide methods on hand for bioinformatics coding work
• c4counter — finds the number and types of complement component 4 (C4) genes in a fasta file. minimap2 is used for mapping
• CampyCPS — Campylobacter CPS relevant gene analysis tool
• charlie — Computational High-throughput Analysis of Repeat Length, Interruptions, Etc.
• climush — Tools to run the CliMush bioinformatics pipeline.
• conodictor — Prediction and classification of conopeptides
• crispr-bean — Base Editor screen analysis [Bayesian Estimation of variant effect] with guide Activity Normalization
• cvmblaster — find antimcirobial resistance genes
• cvmcgmlst — cgMLST analysis tool
• cvmcore — SZQ lab data analysis core function
• cvmtrans — Transposon data process
• Database-comparator — Bioinformatics tool for compering large sequence files
• DNAEncoding — This will return a list of Sequnces and OneHot Encoded Siganl
• ecmpy — Automated construction of enzyme constraint models using ECMpy workflow
• ECMpy2.0 — Automated construction of enzyme constraint models using ECMpy workflow.
• eseq — Process genomic sequences.
• ezqc — EZQC is a streamlined, terminal-based alternative to FastQC.
• fasta-parser — A first try on FASTA files parsing
• fastq2folder — Script to process fastq files before epi2me analysis
• fileunity-seqreads — fileunity for seqreads
• G4SNP — This code finds the distances of SNPs relative to the start codon based on their mRNA positions then executes G4Hunter tool and extracts the closest G4 sequences from the SNPs for several genes.
• gcskewer — A python for plotting GC-skew from DNA sequences.
• getphylo — a python package for automated generation of heuristic phylogenetic trees from genbank files
• gibbs-sampler — Gibbs Sampler for motif discovery
• Giraffe-View — Giraffe_View is specially designed to provide a comprehensive assessment of the accuracy of long-read sequencing datasets obtained from both the PacBio and Nanopore platforms.
• handle-blastn — Handle blastn.
• hkgfinder — find housekeeping genes in prokaryotic (meta)genomic data
• janginfo-organizer — Package for distribution
• jla-demultiplexer — Internal lab use tool for 3 end analysis
• jla-tailer — Tool to find 3' tailing of non-coding RNAs
• kable — A tool for sequence, annotation, and methylome comparison between multiple bacterial genomes
• krisp — A lightweight tool for finding diagnostic regions in whole genome data
• lakeview — A Python library for creating publication-quality genome visualisations.
• lib-dzne-data — Libary for handling data.
• lib-dzne-seq — Libary for handling genetic sequences.
• linkageMapper — Genomic similarities per region
• mdmparis-defense-finder-viz — A helper tool to format data for defense-finder-web visualization from Prodigal and Defense Finder outputs.
• methylbert — A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution
• mrslpred — A tool to predict mRNA subcellular localization
• parett — Python Automated Retrieval of TimeTree data
• picnic-bio — PICNIC (Proteins Involved in CoNdensates In Cells) is a machine learning-based model that predicts proteins involved in biomolecular condensates.
• PointBlaster — find point mutation in assembled genomes
• PrediProt-imports — Additional files for PrediProt
• promotercalculator — Salis Lab's promoter-calculator (Barrick Lab Fork)
• protein-folding-gym-utils — Package with Reinforcement Learning Environments for Protein Folding
• protein-metamorphisms-is — Comprehensive Python Module for Protein Data Management: Designed for streamlined integration and processing of protein information from both UniProt and PDB. Equipped with features for concurrent data fetching, robust error handling, and database synchronization.
• pts1-prediction-tool — Tool for predicting a PTS1 (peroxisomal targeting sequence 1) in a amino acid sequence.
• pykebabs — Easy to use String Kernels for SVM
• relecov-tools — Tools for managing and resolution of buisciii services.
• repmsa — Finding the representetive seq in MSA
• ResBlaster — find antimcirobial resistance genes on genomes
• rhotermpredict — Barrick Lab fork of Salvo 2019 RhoTermPredict
• RiboMetric — A python command-line utility for the generation of comprehensive reports on the quality of ribosome profiling (Ribo-Seq) datasets
• RWexptest — A small example package
• sarand — Tool to extract the neighborhood of the target Antimicrobial Resistance (AMR) genes from the assembly graph.
• sbat — A tool for strand bias analysis of NGS data
• seqreads — seqreads
• StrainFlair — StrainFLAIR (STRAIN-level proFiLing using vArIation gRaph) is a tool for strain identification and quantification that uses variation graph representation of genes sequences
• structuremap — An open-source Python package of the AlphaPept ecosystem
• TwinCons — This projects provides several packages for analysis of MSAs comprised of two sequence groups.
• utils-seq — simple utils for seqs
• utilsovs-pkg — Utils derived from the O-GlcNAc Database source code
• XspecT — Tool to monitor and characterize pathogens using Bloom filters.