Reverse Dependencies of pyfaidx

The following projects have a declared dependency on pyfaidx:

• A2G — Accurarate amplicon alignment to gene consensus
• aMGSIM — aMGSIM: simulate ancient metagenomes for multiple synthetic communities
• anvage — toolkit to process routine operation on gff3, vcf and fasta files
• bamsnap — A converter from .bam to .png for specific genomic region.
• BioSeqTools — A small tool for analyzing biological sequences
• bolero — sequence
• bpnet-lite — bpnet-lite is a minimal implementation of BPNet, a neural network aimed at interpreting regulatory activity of the genome.
• cerebra — finds mutants in your scRNA-seq experiment
• chrombpnet — chrombpnet predicts chromatin accessibility from sequence
• CLASHChimeras — Python package to find chimeras in CRAC/CLASH and HITS-CLIP datasets
• clodius — Tile generation for big data
• CNVkit — Copy number variation toolkit for high-throughput sequencing.
• cooler — Sparse binary format for genomic interaction matrices.
• dcc2 — Dynamic core ortholog compilation tool
• Dellingr — Error supression and variant calling pipeline for Illumina sequencing data
• enformer-dna-diff — This is a package for that combines DeepMind Enformer model with DNA Diffusion project
• enformer-pytorch — Enformer - Pytorch
• extend-orfs — MModule description
• flippyr — Find reference mismatches in PLINK filesets and fix them.
• Galaxy-ML — Galaxy Machine Learning Library
• gencodegenes — Package to load genes from GENCODE GTF files
• genomeplot — A package for simplifying genome-wide plots
• genomepy — Genes and genomes at your fingertips
• gepyto — Utilities and tools to interface with genomic databases and to facilitate common bioinformatics tasks.
• gffutils — Work with GFF and GTF files in a flexible database framework
• gtf2seq — Extract genomic sequences and visualize the genomic features in word document
• guido — no summary
• HugeP2G — Aligning a large number of protein sequences to a genome (use genblasta and genewise)
• imfusion — Tool for identifying transposon insertions in Insertional Mutagenesis screens from gene-transposon fusions using single- and paired-end RNA-sequencing data.
• ivars-test-project — Ivars Test Project
• justblast — Simple program to more efficiently run blast in multicore systems, as well as rough taxonomomic annoation using BASTA LCA
• kipoiseq — kipoiseq: sequence-based data-loaders for Kipoi
• Liftoff — A gene annotation mapping tool
• lifton — Combining DNA and protein alignments to improve genome annotation with LiftOn
• loreme — Extract Methylation calls from ONT or PB long read data
• MHcut — Micro-Homology cut finder
• minorg — Generate minimum gRNA set for multiple non-reference genomes
• mira-multiome — Single-cell multiomics data analysis
• mmsplice — Predict splicing variant effect from VCF
• motif-scraper — Tool for finding degenerate motifs in FASTA files
• mutanno — Mutation Annotation Tool
• Mutation-Simulator — A tool for simulating random mutations in any genome
• mutyper — ancestral k-mer mutation types for SNP data
• nanocompore — Software package that identifies raw signal changes between two conditions from https://github.com/jts/nanopolish resquiggled dRNA-Seq data.
• ncOrtho — Targeted ortholog search for miRNAs
• ont-tombo — Analysis of raw nanopore sequencing data.
• PacbioDataProcessing — Tools to process PacBio sequencing data at molecule level
• panfeed — Compute gene-cluster specific k-mers over a pangenome
• pankmer — Generate a PanGenome given a set of genomes
• peaksql — TODO: add peaksq description
• primer-set-designer — A pipeline for searching species specific primer sets at genome level
• progen-transformer — Protein Generation (ProGen)
• protein-bert — A BERT-like deep language model for protein sequences.
• pyGenomeTracks — Command-line tool to make beautiful and reproducible genome browser snapshots
• pygmes — Run GeneMark-ES using pretrained models
• pyim — Tool for identifying transposon insertions from targeted DNA-sequencing data.
• pyngoST — pyngoST: fast, simultaneous and accurate and multiple sequence typing of Neisseria gonorrhoeae genome collections
• pyranges — GenomicRanges for Python.
• pyranges1 — GenomicRanges for Python.
• pytoda — pytoda: PaccMann PyTorch Dataset Classes.
• pyvariant — Map biological sequence variants (mutations) to their equivalent chromosome, cDNA, gene, exon, protein, and RNA positions.
• refgenconf — A standardized configuration object for reference genome assemblies
• refgenie — Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre-built genomes or build your own for any fasta file
• refget — Python client for refget
• refine-contigs — A simple tool to identify and clean misassemblies for ancient metagenomics
• ribotricer — Python package to detect translating ORFs from Ribo-seq data
• RNFtools — RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
• rostspace — Protein Embedding Visualization Tool.
• rough-graph-mapper — Rough Graph Mapper
• sc2ts — Infer a succinct tree sequence from SARS-CoV-2 sequence alignments
• scAllele — A versatile tool for the detection and analysis of nucleotide variants in scRNA-seq
• scdna-replication-tools — Code for analyzing single-cell replication dynamics
• scgenome — Code for analyzing single cell whole genomes
• seqchromloader — Sequence and chromatin dataloader for deep learning
• seqdataloader — Generate genome-wide classification and regression labels for DNA accessibility data.
• seqiolib — Library to read, write sequence, variants, regions to use them for training of machine learning algorithms.
• seqslab-report-parser — Atgenomix SeqsLab Report Parser
• sequence-qc — Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files
• snprimer — Small python library to search snp in primer by position or by sequence.
• squiggle — DNA Sequence Visualization for Humans.
• str-analysis — Utilities for analyzing short tandem repeats (STRs)
• svviz — A read visualizer for structural variants
• swga — Pipeline to select compatible primer sets for selective whole-genome amplification.
• tangermeme — Biological sequence analysis for the modern age.
• ToolBiox — a biological toolkit for genome assembly, annotation and analysis that we have accumulated from our bioinformatics work
• tral — Detect and evaluate tandem repeats in genomic sequence data.
• trtools — Toolkit for genome-wide analysis of STRs
• UTRme — UTRme
• variant — no summary
• vcf2seq — Inputing a VCF file, it returns the genomic sequence at the specified length (31 by default).
• vcfsynonymous — Detect synonymous genetic variants in VCF
• vespa-effect — Predictor for single-amino acid variant effects in protein sequences (https://doi.org/10.1007/s00439-021-02411-y)
• vica — find highly divergent DNA and RNA viruses in microbiomes
• whatshap — phase genomic variants using DNA sequencing reads
• wisestork — Within-sample CNV calling