R-universe search: bigwig

bioc

megadepth:megadepth: BigWig and BAM related utilities

This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.

Maintained by David Zhang. Last updated 3 months ago.

software coverage dataimport transcriptomics rnaseq preprocessing bam bigwig daspter megadepth recount2 recount3

18.2 match 12 stars 6.69 score 7 scripts 3 dependents

bioc

ORFik:Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Maintained by Haakon Tjeldnes. Last updated 28 days ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

9.6 match 33 stars 10.63 score 115 scripts 2 dependents

bioc

derfinder:Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

Maintained by Leonardo Collado-Torres. Last updated 3 months ago.

differentialexpression sequencing rnaseq chipseq differentialpeakcalling software immunooncology coverage annotation-agnostic bioconductor derfinder

6.5 match 42 stars 10.03 score 78 scripts 6 dependents

junjunlab

transPlotR:Visualize Transcript Structures in Elegant Way

To visualize the gene structure with multiple isoforms better, I developed this package to draw different transcript structures easily.

Maintained by Jun Zhang. Last updated 2 years ago.

bed bigwig gene linkvis transcript visualization

11.0 match 73 stars 5.34 score 60 scripts

bioc

rtracklayer:R interface to genome annotation files and the UCSC genome browser

Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

Maintained by Michael Lawrence. Last updated 8 days ago.

annotation visualization dataimport zlib openssl curl

4.5 match 12.66 score 6.7k scripts 481 dependents

bioc

seqsetvis:Set Based Visualizations for Next-Gen Sequencing Data

seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

Maintained by Joseph R Boyd. Last updated 3 months ago.

software chipseq multiplecomparison sequencing visualization

8.8 match 5.82 score 82 scripts

bioc

plyranges:A fluent interface for manipulating GenomicRanges

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

Maintained by Michael Love. Last updated 5 months ago.

infrastructure datarepresentation workflowstep coverage bioconductor data-analysis dplyr genomic-ranges genomics tidy-data

4.0 match 143 stars 12.60 score 1.9k scripts 20 dependents

bioc

CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Maintained by Malte Thodberg. Last updated 5 months ago.

software transcription coverage geneexpression generegulation peakdetection dataimport datarepresentation transcriptomics sequencing annotation genomebrowsers normalization preprocessing visualization

5.4 match 8 stars 7.46 score 67 scripts 1 dependents

bioc

chevreulShiny:Tools for managing SingleCellExperiment objects as projects

Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Maintained by Kevin Stachelek. Last updated 13 days ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

6.0 match 5.08 score

bioc

recount3:Explore and download data from the recount3 project

The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.

Maintained by Leonardo Collado-Torres. Last updated 3 months ago.

coverage differentialexpression geneexpression rnaseq sequencing software dataimport annotation-agnostic bioconductor count derfinder exon gene human illumina junction mouse recount recount3

3.8 match 33 stars 8.03 score 216 scripts

bioc

GenomicPlot:Plot profiles of next generation sequencing data in genomic features

Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. 'GenomicPlot' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.

Maintained by Shuye Pu. Last updated 2 months ago.

alternativesplicing chipseq coverage geneexpression rnaseq sequencing software transcription visualization annotation

4.6 match 3 stars 5.62 score 4 scripts

rnabioco

cpp11bigwig:Read bigWig and bigBed Files

Read bigWig and bigBed files using "libBigWig" <https://github.com/dpryan79/libBigWig>. Provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group.

Maintained by Jay Hesselberth. Last updated 8 days ago.

cpp

5.8 match 3.95 score 3 scripts 1 dependents

bioc

chevreulProcess:Tools for managing SingleCellExperiment objects as projects

Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Maintained by Kevin Stachelek. Last updated 1 months ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

4.3 match 5.38 score 2 scripts 2 dependents

stuart-lab

Signac:Analysis of Single-Cell Chromatin Data

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Maintained by Tim Stuart. Last updated 7 months ago.

atac bioinformatics single-cell zlib cpp

1.9 match 349 stars 12.19 score 3.7k scripts 1 dependents

bioc

igvR:igvR: integrative genomics viewer

Access to igv.js, the Integrative Genomics Viewer running in a web browser.

Maintained by Arkadiusz Gladki. Last updated 5 months ago.

visualization thirdpartyclient genomebrowsers

2.5 match 43 stars 8.31 score 118 scripts

tanaylab

misha:Toolkit for Analysis of Genomic Data

A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) <doi:10.1038/ng.947>.

Maintained by Aviezer Lifshitz. Last updated 6 days ago.

genomic-data-analysis cpp

3.3 match 4 stars 5.86 score

bioc

plotgardener:Coordinate-Based Genomic Visualization Package for R

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Maintained by Nicole Kramer. Last updated 5 months ago.

visualization genomeannotation functionalgenomics genomeassembly hic cpp

1.8 match 308 stars 10.16 score 167 scripts 3 dependents

rnabioco

valr:Genome Interval Arithmetic

Read and manipulate genome intervals and signals. Provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data. Riemondy et al. (2017) <doi:10.12688/f1000research.11997.1>.

Maintained by Kent Riemondy. Last updated 7 days ago.

bedtools genome interval-arithmetic cpp

1.8 match 90 stars 9.69 score 227 scripts

bioc

CNEr:CNE Detection and Visualization

Large-scale identification and advanced visualization of sets of conserved noncoding elements.

Maintained by Ge Tan. Last updated 5 months ago.

generegulation visualization dataimport

1.8 match 3 stars 9.28 score 35 scripts 19 dependents

bioc

wiggleplotr:Make read coverage plots from BigWig files

Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.

Maintained by Kaur Alasoo. Last updated 5 months ago.

immunooncology coverage rnaseq chipseq sequencing visualization geneexpression transcription alternativesplicing

2.9 match 5.49 score 26 scripts 1 dependents

bioc

methrix:Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

Maintained by Anand Mayakonda. Last updated 5 months ago.

dnamethylation sequencing coverage bedgraph bioinformatics dna-methylation

1.9 match 31 stars 7.51 score 39 scripts 1 dependents

bioc

methylKit:DNA methylation analysis from high-throughput bisulfite sequencing results

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.

Maintained by Altuna Akalin. Last updated 16 days ago.

dnamethylation sequencing methylseq genome-biology methylation statistical-analysis visualization curl bzip2 xz-utils zlib cpp

1.2 match 220 stars 11.80 score 578 scripts 3 dependents

bioc

ELMER:Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Maintained by Tiago Chedraoui Silva. Last updated 5 months ago.

dnamethylation geneexpression motifannotation software generegulation transcription network

1.7 match 7.42 score 176 scripts

bioc

metaseqR2:An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Maintained by Panagiotis Moulos. Last updated 5 days ago.

software geneexpression differentialexpression workflowstep preprocessing qualitycontrol normalization reportwriting rnaseq transcription sequencing transcriptomics bayesian clustering cellbiology biomedicalinformatics functionalgenomics systemsbiology immunooncology alternativesplicing differentialsplicing multiplecomparison timecourse dataimport atacseq epigenetics regression proprietaryplatforms genesetenrichment batcheffect chipseq

1.9 match 7 stars 6.05 score 3 scripts

bioc

alabaster.files:Wrappers to Save Common File Formats

Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

Maintained by Aaron Lun. Last updated 5 months ago.

datarepresentation dataimport

2.5 match 4.50 score 21 scripts

bioc

esATAC:An Easy-to-use Systematic pipeline for ATACseq data analysis

This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.

Maintained by Zheng Wei. Last updated 5 months ago.

immunooncology sequencing dnaseq qualitycontrol alignment preprocessing coverage atacseq dnaseseq atac-seq bioconductor pipeline cpp openjdk

1.8 match 23 stars 6.11 score 3 scripts

bioc

ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

Maintained by Pacome Prompsy. Last updated 5 months ago.

shinyapps software singlecell chipseq atacseq methylseq classification clustering epigenetics principalcomponent annotation batcheffect multiplecomparison normalization pathways preprocessing qualitycontrol reportwriting visualization genesetenrichment differentialpeakcalling epigenomics shiny single-cell cpp

1.7 match 14 stars 5.83 score 16 scripts

bioc

chevreulPlot:Plots used in the chevreulPlot package

Tools for plotting SingleCellExperiment objects in the chevreulPlot package. Includes functions for analysis and visualization of single-cell data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Maintained by Kevin Stachelek. Last updated 17 days ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

1.7 match 5.08 score 2 scripts

bioc

wavClusteR:Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).

Maintained by Federico Comoglio. Last updated 5 months ago.

immunooncology sequencing technology ripseq rnaseq bayesian

1.9 match 4.60 score 3 scripts

bioc

SpliceWiz:interactive analysis and visualization of alternative splicing in R

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.

Maintained by Alex Chit Hei Wong. Last updated 4 days ago.

software transcriptomics rnaseq alternativesplicing coverage differentialsplicing differentialexpression gui sequencing cpp openmp

1.3 match 16 stars 6.41 score 8 scripts

bioc

recount:Explore and download data from the recount project

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Maintained by Leonardo Collado-Torres. Last updated 3 months ago.

coverage differentialexpression geneexpression rnaseq sequencing software dataimport immunooncology annotation-agnostic bioconductor count derfinder deseq2 exon gene human illumina junction recount

0.8 match 41 stars 9.57 score 498 scripts 3 dependents

bioc

groHMM:GRO-seq Analysis Pipeline

A pipeline for the analysis of GRO-seq data.

Maintained by Tulip Nandu. Last updated 2 days ago.

sequencing software

1.6 match 1 stars 4.48 score 25 scripts

bioc

tracktables:Build IGV tracks and HTML reports

Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.

Maintained by Tom Carroll. Last updated 5 months ago.

sequencing reportwriting

1.8 match 3.87 score 37 scripts

bioc

rGenomeTracks:Integerated visualization of epigenomic data

rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.

Maintained by Omar Elashkar. Last updated 5 months ago.

software hic visualization

2.0 match 3.30 score 2 scripts

bioc

genomation:Summary, annotation and visualization of genomic data

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Maintained by Altuna Akalin. Last updated 5 months ago.

annotation sequencing visualization cpgisland cpp

0.5 match 75 stars 11.09 score 738 scripts 5 dependents

bioc

epistack:Heatmaps of Stack Profiles from Epigenetic Signals

The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.

Maintained by DEVAILLY Guillaume. Last updated 5 months ago.

rnaseq preprocessing chipseq geneexpression coverage bioinformatics

0.5 match 6 stars 5.26 score 5 scripts

bioc

soGGi:Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.

Maintained by Tom Carroll. Last updated 5 months ago.

sequencing chipseq coverage

0.5 match 4.49 score 51 scripts 1 dependents

bioc

profileplyr:Visualization and annotation of read signal over genomic ranges with profileplyr

Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

Maintained by Tom Carroll. Last updated 5 months ago.

chipseq dataimport sequencing chiponchip coverage

0.5 match 4.03 score 54 scripts