Reverse Dependencies of pyBigWig

The following projects have a declared dependency on pyBigWig:

• allcools — Toolkit for single-cell DNA methylome and multiomic data analysis.
• atacworks — NVIDIA genomics python libraries and utiliites
• avocado-epigenome — Avocado is a package for learning a latent representation of the human epigenome.
• bam2bw — A command-line tool for converting SAM/BAM files into stranded bp resolution BigWig files.
• biodatatools — A python package with useful biological data processing methods
• bolero-process — Data preprocessing for bolero package
• 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
• bw-merge-window — A python extension for quick access to bigWig and bigBed files.
• bwread — Read bigwig files into Python data science formats.
• candig-server — Server implementation of the CanDIG APIs
• CAVA — CAVA (Clinical Annotation of VAriants)
• cLoops2 — Loop-calling and peak-calling for sequencing-based interaction data, including related analysis utilities.
• cobind — collocation analysis of genomics intervals
• corigami — C.Origami: cell type-specific chromatin structure prediction.
• corigami-demo — C.Origami: cell type-specific chromatin structure prediction.
• CRADLE — Correct Read Counts and Analysis of Differently Expressed Regions
• crispr-bean — Base Editor screen analysis [Bayesian Estimation of variant effect] with guide Activity Normalization
• CrossMap — CrossMap -- Lift over genomics coordinates between assemblies.
• daric — DARIC, a computational framework to find quantitatively differential compartments from Hi-C data
• dataintegrator — Python data processing and formatting tools for gwas summary stats
• decoil — EcDNA reconstruction from long-read nanopore data
• deepTools — Useful tools for exploring deep sequencing data.
• DISPbind — Disorder protein genomic binding analysis toolkit
• dragonnfruit — dragonnfruit is a method for analyzing scATAC-seq experiments.
• easyliftover — A python package for lifting over biological files
• enformer-dna-diff — This is a package for that combines DeepMind Enformer model with DNA Diffusion project
• epiout — EpiOut: outlier detection for DNA accesibility data.
• epiprofile — Epidaurus is a program to visualize the epigenomic landscape of genomic regions of interest (TF bindings, TSS, etc).
• FinaleToolkit — FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
• fseq2 — Improving the feature density based peak caller with dynamic statistics.
• GC-analysis — A program that compute the GC percentage of a given genomic sequence
• geniml — Genomic interval toolkit
• genomedashboard — Genome Dashboard is the logic behind a web-based prototype of a genomics dashboard, specifically designed to integrate informatics and 4D material studies of chromatin. Genome Dashboard unites our Interactive Chromatin Modeling (ICM) tools with the Biodalliance genome browser and the JSMol molecular viewer to rapidly fold any DNA sequence into atomic or coarse-grained models of DNA, nucleosomes or chromatin.
• genomedata — tools for accessing large amounts of genomic data
• genomenotebook — A genome browser in your Jupyter notebook
• genomeview — genomeview
• GenomicArrays — Genomic region based arrays backed by TileDB
• genomkit — genomkit
• genvarloader — Pipeline for efficient genomic data processing.
• gReLU — gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences
• HiCExplorer — Set of programs to process, analyze and visualize Hi-C data
• HiCPlot — plot heatmaps from Hi-C matrix and tracks from bigwig files
• hisv — A computational pipeline for structural variation detection from Hi-C data
• howard-ann — HOWARD - Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery
• janggu — Utilities and datasets for deep learning in genomics
• keras-dna — Build keras generator for genomic application
• kerasAC — keras Accessibility Models (kerasAC)
• lakeview — A Python library for creating publication-quality genome visualisations.
• lanceotron — Command-line interface to the lanceotron deep learning peak caller
• lapa — Tools for alternative polyadenylation detection and analysis from diverse data sources (3'seq and long-reads) and transcript start site detection and analysis from long-read RNA-seq.
• mbf-fileformats — various file formats
• mbf-genomics — All about intervals on genomic data
• methrafo — MeDIP-Seq Methylation Level Random-forest based Estimator
• moca — Tool for motif conservation analysis
• modbamtools — A set of tools to manipulate and visualize data from base modification bam files
• momics — A package to create and manage genome-related TileDB arrays
• MultiMM — A tool for chromatin modeling from nucleosomes to chromosomal territories.
• nasap — This is nASAP setup file
• PEALS — Peak-based Enhancement Analysis PipeLine for MeRIP-seq
• psite — Model-based inference of P-site offsets
• pycallingcards — "Calling cards data analysis in Python."
• pyGenomeTracks — Command-line tool to make beautiful and reproducible genome browser snapshots
• pyPINTS — Peak Identifier for Nascent Transcripts Starts (PINTS)
• pyranges1 — GenomicRanges for Python.
• qtl — Utilities for analyzing and visualizing QTL data
• rmsp-gui — Resource management system GUI for python
• rocco — Robust ATAC-seq Peak Calling for Many Samples via Convex Optimization
• RSeQC — QC package for RNA-seq data.
• sc3dg — A toolkit for processing single cell Hi-C data
• scatac_fragment_tools — Tools for working with scATAC-seq fragment files.
• scce — a Single-cell method for predicting Chromatin Conformation based on gene Expression
• scdna-replication-tools — Code for analyzing single-cell replication dynamics
• scgenome — Code for analyzing single cell whole genomes
• schickit — a toolkit for processing single cell Hi-C data
• seqchromloader — Sequence and chromatin dataloader for deep learning
• seqdata — Annotated sequence data
• seqdataloader — Generate genome-wide classification and regression labels for DNA accessibility data.
• singlecellmultiomics — Tools to deal with one or more measurements from single cells
• SIRVsuite — SIRVsuite - a command line tool to QC an RNA-Seq workflow using Lexogen's SIRV spike-in controls
• spiker — spiker (Analysis workflow for ChIP-seq data with spike-in)
• str-analysis — Utilities for analyzing short tandem repeats (STRs)
• tangermeme — Biological sequence analysis for the modern age.
• tbsp — SNP-based trajectory inference
• trackC — no summary
• trackplot — The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/
• ugbio-core — Ultima Genomics core bioinfo utils
• wgba — Which genome build again?
• zzx-deep-genome — A module for constructing parameter initialization matrix of convolutional neural network for genomics using PFM matrix information of transcription factors in Jaspar database.