Reverse Dependencies of biopython
The following projects have a declared dependency on biopython:
- chewBBACA-NServer — chewBBACA comunicates with the nomenclature server HUUURRR
- ChromoPhyloGen — A package for inferring CNA fitness evolutionary trees and CNAs' evolutionary efficiency.
- Circle-Map — Circular DNA analysis tools
- circtools — circtools - a circular RNA toolbox
- circulocov — Circular-Aware Coverage for Draft Genomes
- CIRI-long — circular RNA identification from Nanopore
- cirtap — A CLI to handle PATRIC data from the FTP
- CLASHChimeras — Python package to find chimeras in CRAC/CLASH and HITS-CLIP datasets
- cldfviz — A cldfbench plugin to create vizualisations of CLDF datasets
- click-demultiplex — Command Line Tool to Demultiplex a paired-end fastq file into several fastq files,
- clinker — no summary
- clinker-windows — no summary
- clipkit — Alignment trimming software for phylogenetics.
- clld-etymology-plugin — Display cognate sets in CLLD apps.
- cloudmol — Easily protein folding and design with cloudmol
- clumps-ptm — CLUMPS-PTM driver gene discovery using 3D protein structure (Getz Lab).
- cluseek — A GUI application for finding and categorizing gene clusters found in the NCBI GenBank genomic database.
- cluster-depp-test — DEPP: Deep Learning Enables Extending Species Trees using Single Genes
- cmonkey2 — cmonkey2 is an implementation of the cmonkey biclustering method in Python
- CMSeq — Set of utilities on sequences and BAM files
- CNAsim — CNAsim is a software package for simulation of single-cell CNA data from tumors.
- CNVkit — Copy number variation toolkit for high-throughput sequencing.
- cobra-meta — COBRA (Contig Overlap Based Re-Assembly) is a bioinformatics tool to get higher quality viral genomes assembled from metagenomes of short paired-end reads. COBRA was written in Python. COBRA has so far only been tested on assembled contigs from metaSPAdes, IDBA_UD, and MEGAHIT.
- cockatoo-genome — Cockatoo - intelligent clustering of metagenomic samples for coassembly
- cocopye — Feature-based prediction of genome quality indices
- codon-degeneracy — Routines for the extraction of degenerate sides and estimation of numbers neutral substitutions from sequences and alignments.
- CodonU — An integrated package for codon usage analysis
- codx — A package used to retrieve exon for protein sequences from RefSeqGene database
- colabfold — Making protein folding accessible to all. Predict proteins structures both in google colab and on your machine
- colabtestingpkg — no summary
- colorclade — colorclade draws phylogenies with hierarchical coloring for easier visual comparison.
- combined-gene-caller — Combined gene caller for MGnify pipeline, to combine predictions from FragGeneScan and Prodigal
- community-dashboard-plots — no summary
- comp_dnds — Efficiently computing dN/dS according to the NJ86 method
- complexcgr — complex Chaos Game Representation for DNA
- condiga — ConDiGA: Contigs directed gene annotation for accurate protein sequence database construction in metaproteomics
- configure-dms-viz — Configure your data for visualization with dms-viz.github.io
- contig-tools — Utility package to parse multi fasta files resulting from de novo assembly
- ContigNet — ContigNet, a deep learning based phage-host interaction prediction tool
- COnTORT — COnTROT (COmprehensive Transcriptomic ORganizational Tool) is a program that will download and organize all expression data in GEO related to a search result, commonly an organism.
- cooler — Sparse binary format for genomic interaction matrices.
- Corekaburra — A commandline bioinformatics tool to utilize syntenic information from genomes in the context of pan-genomes
- correlationPlus — A Python package to calculate, visualize and analyze correlations of proteins.
- cortexpy — The python sister project to CortexJDK
- countASAP — A software for converting ASAPseq FASTQs to count matrices
- covid-spike-classification — Detect interesting SARS-CoV-2 spike protein variants from Sanger sequencing data.
- covigator — no summary
- covpipe — Sars-Cov-2 NGS Pipline for generating consensus sequences
- covsonar — A database-driven system for handling genomic sequences and screening genomic profiles.
- CPT-GFFParser — A Biopython extension package for I/O of GFF files
- crabs — CRABS: Creating Reference databases for Amplicon-Based Sequencing
- cradlebio — Client for Cradle's Alphafold-as-a-service
- crazydoc — Read genetic sequences from stylized docx files
- crecombio — Site-specific DNA recombination simulator
- crimm — Chemistry with the ReInvented Macromolecular
- crispector2 — CRISPECTOR2 - Genome Editing Analysis Tool, with allele extension
- crispr-ambiguous-mapping — no summary
- crispr-be-sensor — no summary
- crispr-library-prep — no summary
- crispr-millipede — no summary
- crispr-millipede-coding — no summary
- crispr-millipede-helper — no summary
- crispr-screen — crispr_tools - Analysis Tools for CRISPR Screen Design and Analysis
- crispr-tools — crispr_tools - Analysis Tools for CRISPR Screen Design and Analysis
- crisprbact — Tools to design and analyse CRISPRi experiments
- csstar — fetches version name from file, otherwise reports non-numeric string
- CSTB-core — Utility function for io and word searching and indexing
- cubat — CUBAT -- CUB Analysis Toolkit
- cugg — Modules for LD computing, liftover and region extraction
- culebrONT — CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple
- Curare — Curare: A Customizable and Reproducible Analysis Pipeline for RNA-Seq Experiments
- curatedmetagenomicdataloader — PyTorch DataLoader for curatedMetagenomicData
- cuteFC — Regenotyping structural variants through an accurate and efficient force-calling method
- cuteSV — Long-read-based human genomic structural variation detection with cuteSV
- cuttlery — Codon Usage Table Tools-lery.
- cytolncpred — A tool to predict probability of lncRNA localizing to Cytoplasm
- d3r — Drug Design Data Resource CELPP Runner is an application to run the filtering, docking, and evaluation of new sequences from wwpdb
- dasi — Automated DNA assembly planner for Python
- dbotu — Distribution-based OTU calling
- dbvirus-searcher — SRA data searcher w/ local caching for the DBVirus project
- dcc2 — Dynamic core ortholog compilation tool
- dcicwrangling — Scripts and Jupyter notebooks for 4DN wrangling
- dcma — Deep Codon Mutation Analyser
- ddgun — DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations (https://doi.org/10.1186/s12859-019-2923-1)
- deciphon-api — RESTful API for Deciphon scheduler
- deepaclive — Detecting novel pathogens from NGS reads in real-time during a sequencing run.
- DeepARG — no summary
- deepbgc — DeepBGC - Biosynthetic Gene Cluster detection and classification
- deepnog — Deep learning tool for protein orthologous group assignment
- DeepRank-GNN — Graph Neural network Scoring of protein-protein conformations
- DeepSecE — A Deep Learning Framework for Multi-class Secreted Effector Prediction in Gram-negative Bacteria.
- deepsig-biocomp — DeepSig - Predictor of signal peptides in proteins based on deep learning
- deepsmirud — deepsmirud
- demort — DEmultiplexing MOnitoring Report Tool
- demultiplexer — python script to demultiplex illumina reads tagged with the leeselab tagging scheme
- depht — Discovery and Extraction of Phages Tool
- depp — DEPP: Deep Learning Enables Extending Species Trees using Single Genes
- depp-test — DEPP: Deep Learning Enables Extending Species Trees using Single Genes
- derep-genomes — A simple genome de-replication tool with fastANI
- deTELpy — Python package of the deTEL translation error detection pipeline from mass-spectrometry data