Reverse Dependencies of pybedtools

The following projects have a declared dependency on pybedtools:

• allcools — Toolkit for single-cell DNA methylome and multiomic data analysis.
• ataqc — ATAqC - quality control for ATAC-seq
• bio-jtools — Various bioinformatics tools in one package
• biobit — Rust-powered Python library for biological data analysis
• blockify — Fast and optimal genome segmentation with Bayesian blocks
• bpnet — BPNet: toolkit to learn motif synthax from high-resolution functional genomics data using convolutional neural networks
• Broad-GenePy — A useful module for any CompBio
• capatsv — Cellranger ATAC Peak Annotation, sourced from Cellranger ATAC v2.1.0
• capcruncher — An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data
• CAVA — CAVA (Clinical Annotation of VAriants)
• cgbeacon2 — A beacon supporting GA4GH API 1.0
• chame — Chromatin accessibility module
• chess-hic — Quantitative comparison and automatic feature extraction for chromatin contact data.
• CIRCexplorer2 — Circular RNA analysis toolkits
• Circle-Map — Circular DNA analysis tools
• circtools — circtools - a circular RNA toolbox
• DAStk — Differential ATAC-seq toolkit
• decoil — EcDNA reconstruction from long-read nanopore data
• delfies — delfies is a tool for the detection of DNA Elimination breakpoints
• dictys — Context specific and dynamic gene regulatory network reconstruction and analysis
• dismotif — disrupted motifs
• DISPbind — Disorder protein genomic binding analysis toolkit
• DriverPower — Combined burden and functional test for coding and noncoding cancer drivers
• epiVIA — Virial Integration Analysis with epigenetic data
• eQTac — The eQTac method.
• finrich — Calculate enrichment of genomic regions with fine-mapping signals
• flair-brookslab — flair
• fseq2 — Improving the feature density based peak caller with dynamic statistics.
• fstitch-annotate — Provides additional annotation tools using FStitch segment data.
• FStitch-Bidir — Annotates bidirections using FStitch segment data.
• garfield — Garfield: Graph-based Contrastive Learning enable Fast Single-Cell Embedding
• GarNet — no summary
• gene4mvcf — Description of your package
• genome-downloader — A package to download genome, annotations and bowtie2 indexes
• genomics-data-index — Indexes genomics data (nucleotide variants, kmers, MLST) for fast querying of features.
• hichub — Comprehensive Network Analysis for HiC
• hmmCDR — Find CDR locations using bedmethyl file and CenSat annotations. (REQUIRES BEDTOOLS INSTALLED)
• imaps — Bioinformatic pipelines for analysis of CLIP data
• ImputeHiFI — no summary
• inferelator-prior — Inferelator-Prior Network Generation Tool
• intron — Intron retention tool
• iRRBS — RRBS tool for deleting artificial cytosins
• janggu — Utilities and datasets for deep learning in genomics
• jcvi — Python utility libraries on genome assembly, annotation and comparative genomics
• keras-dna — Build keras generator for genomic application
• kipoi_datasets — kipoi_datasets: training datasets for genomics
• kipoi_veff — kipoi_veff: variant effect prediction plugin for Kipoi
• kipoiseq — kipoiseq: sequence-based data-loaders for Kipoi
• ldsc — LD Score Regression (LDSC)
• levseq — no summary
• LingerGRN — Gene regulatory network inference
• loreme — Extract Methylation calls from ONT or PB long read data
• Magphi — A bioinformatics tool allowing for examnination and extraction of genomic features using seed sequences.
• MATES — no summary
• miasort — A Tool for Multiplex Chromatin Interaction Analysis by Efficiently Sorting Chromatin Complexes
• midasv3 — https://midas2.readthedocs.io/en/latest/
• mimseq — Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
• minorg — Generate minimum gRNA set for multiple non-reference genomes
• moca — Tool for motif conservation analysis
• MultiGATE — MultiGATE single cell
• muon — Multimodal omics analysis framework
• nanome-jax — NANOME (Nanopore methylation) pipeline developed by Li Lab at The Jackson Laboratory
• ngs-test-utils — Utilities for generation of synthetic NGS files
• ngs-toolkit — A toolkit for NGS analysis with Python.
• ngsscriptlibrary — Scripts for NGS data-analysis
• pankmer — Generate a PanGenome given a set of genomes
• papolarity — Papolarity is a tool to analyze polarity of transcriptomic alignments such as Ribo-seq and RNA-seq.
• peaks2utr — A robust, parallelized Python CLI for annotating three_prime_UTR
• pipeclip — PIPELINE FOR CLIP SEQ DATA
• py-popgen — Software platform for facilitating population genomic analyses
• pycallingcards — "Calling cards data analysis in Python."
• 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
• pyPINTS — Peak Identifier for Nascent Transcripts Starts (PINTS)
• regsnp-intron — Predict disease-causing probability of human intronic SNVs.
• rocco — Robust ATAC-seq Peak Calling for Many Samples via Convex Optimization
• rosewater — Expression-aware gene assignment of ROSE output.
• scape-apa — A package for estimating alternative polyadenylation events from scRNA-seq data.
• scButterfly — A versatile single-cell cross-modality translation method via dual-aligned variational autoencoders
• sccross — Single cell multi-omics cross modal generation, multi-omics simulation and perturbation
• scglue — Graph-linked unified embedding for unpaired single-cell multi-omics data integration
• scikit-ribo — A scikit framework for joint analysis of Riboseq and RNAseq data
• scverse — scverse bundle
• segzoo — System for turnkey analysis of semi-automated genome annotations
• seqchromloader — Sequence and chromatin dataloader for deep learning
• seqdata — Annotated sequence data
• seqdataloader — Generate genome-wide classification and regression labels for DNA accessibility data.
• sequence-qc — Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files
• slamdunk — SLAMdunk suite for analyzing SLAM-seq data
• smap-effect-prediction — no summary
• splam — Splice junction scoring tool
• targeneintersect — Use pybedtools intersect to gain target gene information in pandas dataframes
• tigmint — Correct misassemblies using linked reads
• trand — 'Transcript Distances'
• utrcalling — Package with tools to calculate molecule UTR sizes from RNA sequencing reads.
• vafator — Annotate a VCF file with AF, AD and DP from tumor and normal BAMs
• XICRA — Small RNAseq pipeline for paired-end reads
• XYalign — Command line tools and python library to infer ploidy, correct for sex chromosome complement, and work with NGS data
• ZeaGeneMap — A python tool for identifying the mapping of genes between two genomes.