Reverse Dependencies of bio

The following projects have a declared dependency on bio:

• AltAnalyze3 — AltAnalyze3: Advanced RNA-Seq Analysis Workflow
• aphylogeo — A phylogenetic and geographic analysis tool
• APSCALE-blast — Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - BLAST application
• 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
• bio-anglerfish — Anglerfish, a tool to demultiplex Illumina libraries from ONT data
• BIOecmpy — Automated construction of enzyme constraint models using ECMpy workflow
• biofile — Process various file format for RNA-Seq data analysis
• bioinformatics-tools — Simple tools for common bioinformatic use-cases
• bioomics — Download, retrieve and process omics data for further bioinformatics
• biosequtils — Provide methods on hand for bioinformatics coding work
• boldigger3 — A python package to query different databases of boldsystems.org v5!
• bsxplorer — Analytical framework for BS-seq data comparison and visualization
• 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
• DeepTranSyT — Transporters annotation using LLM's
• 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.
• egger — a python package for graphing emapper results
• 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
• handle-blastn — Handle blastn.
• hkgfinder — find housekeeping genes in prokaryotic (meta)genomic data
• hmmstuff — A tool to get structural information about light chain amyloids
• 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.
• levseq — no summary
• 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 — no summary
• miniwalk — miniwalk is a tool for genotyping SVs from minigraph .gfa graphs
• mrslpred — A tool to predict mRNA subcellular localization
• multiversity — Package that includes the code related to the Multiplex Classification Approach and the MultiCaRe dataset.
• parett — Python Automated Retrieval of TimeTree data
• PhyloFunc — calculating protein- level functional distances
• picnic-bio — PICNIC (Proteins Involved in CoNdensates In Cells) is a machine learning-based model that predicts proteins involved in biomolecular condensates.
• PlasMap — no summary
• PointBlaster — find point mutation in assembled genomes
• PrediProt-imports — Additional files for PrediProt
• 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.
• proteusPy — proteusPy - Protein Structure Analysis and Modeling Tools
• pts1-prediction-tool — Tool for predicting a PTS1 (peroxisomal targeting sequence 1) in a amino acid sequence.
• pydisconet — analyzing the co-authorship network of researchers in the field of biology
• pykebabs — Easy to use String Kernels for SVM
• pymibig — A small tool to download, match and save sequences from MIBiG.
• relecov-tools — Tools for managing and resolution of buisciii services.
• repmsa — Finding the representetive seq in MSA
• ResBlaster — find antimcirobial resistance genes on genomes
• RiboMetric — A python command-line utility for the generation of comprehensive reports on the quality of ribosome profiling (Ribo-Seq) datasets
• rohittools — Analysis of single-cell Massively Parallel Reporter Assay (MPRA) data
• 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
• scprint — scPRINT is a Large Cell Model for Gene Network Inference, Denoising and more from scRNAseq 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.
• ugbio-single-cell — Ultima Genomics Single Cell utils
• utils-seq — simple utils for seqs
• utilsovs-pkg — Utils derived from the O-GlcNAc Database source code
• xgdl — Explainability Library with Geometric Deep Learning for Scientific Tasks
• XspecT — Tool to monitor and characterize pathogens using Bloom filters.
• yEscher — Run gene knockouts and analyize S. Cerevisae, built on top of yeastGEM
• zeny-mut — detect mutation in gene and its location
• zoDIAq — Bioinformatics software package for identifying peptides and proteins in DIA and DISPA mass spectrometry data files.