Reverse Dependencies of gffutils

The following projects have a declared dependency on gffutils:

• aimap — aimap provides a package and script for finding the modification from Adenosine to inosine (A to I).
• anvage — toolkit to process routine operation on gff3, vcf and fasta files
• BioCantor — Flexible feature arithmetic, seamlessly integrated with nested coordinate systems.
• cblaster — no summary
• ce-detector — A program used to detect Cryptic Exon.
• chado-tools — Tools to access CHADO databases
• clinker — no summary
• clinker-windows — no summary
• collect-columns — Retrieve a column for each in a set of tables, placing them in a single output table.
• Corekaburra — A commandline bioinformatics tool to utilize syntenic information from genomes in the context of pan-genomes
• deduce-uces — DedUCE is a tool for efficiently finding ultra-conserved elements across multiple genomes.
• emapper2gbk — Build .gbk files starting from eggnog annotation files and genomes (fasta)
• enformer-dna-diff — This is a package for that combines DeepMind Enformer model with DNA Diffusion project
• gene-cluster-matrix — Visualization library for gene cluster & distance
• gene-normalizer — VICC normalization routine for genes
• geneplot — Plot gene intron/exon topology, protein domains and SNPs
• jcvi — Python utility libraries on genome assembly, annotation and comparative genomics
• jla-tailer — Tool to find 3' tailing of non-coding RNAs
• kipoiseq — kipoiseq: sequence-based data-loaders for Kipoi
• kocher-tools — Bioinformatic Tools for the Kocher Lab
• Liftoff — A gene annotation mapping tool
• lifton — Combining DNA and protein alignments to improve genome annotation with LiftOn
• midas2 — https://midas2.readthedocs.io/en/latest/
• mmsplice — Predict splicing variant effect from VCF
• mpwt — Multiprocessing for Pathway Tools
• MutTui — A pipeline to reconstruct mutational spectra for bacterial and viral datasets
• omniclip — no summary
• peaks2utr — A robust, parallelized Python CLI for annotating three_prime_UTR
• proksee-batch — Proksee Batch
• pyeasyfuse — EasyFuse is a pipeline to detect fusion transcripts from RNA-seq data with high accuracy.
• pyGenomeTracks — Command-line tool to make beautiful and reproducible genome browser snapshots
• pyNextGen — [UNSTABLE] A package of custom tools to tackle bioinformatic projects.
• pypgatk — Python tools for proteogenomics
• RCK — A tool for (R)econstruction of (C)ancer (K)aryotypes (both clone- and haplotype-specific)
• refineGEMs — refineGEMs: a python package intended to help with the curation of genome-scale metabolic models (GEMS)
• riboloco — Riboseq analysis
• ScanCE — A computational workflow for cryptic exon identification in RNA-seq data.
• scanexitronlr — ScanExitronLR: a lightweight tool for the characterization and quantification of exitrons in long read RNA-seq data
• scape-apa — A package for estimating alternative polyadenylation events from scRNA-seq data.
• scikit-ribo — A scikit framework for joint analysis of Riboseq and RNAseq data
• splam — Splice junction scoring tool
• tns-piler — Tool for finding cumulative pileups
• torchcell — An example package
• transcriptionary — transcript plots
• vcfsynonymous — Detect synonymous genetic variants in VCF