R-universe search: genomicvariation

bioc

infercnv:Infer Copy Number Variation from Single-Cell RNA-Seq Data

Using single-cell RNA-Seq expression to visualize CNV in cells.

Maintained by Christophe Georgescu. Last updated 5 months ago.

software copynumbervariation variantdetection structuralvariation genomicvariation genetics transcriptomics statisticalmethod bayesian hiddenmarkovmodel singlecell jags cpp

10.0 match 595 stars 10.91 score 674 scripts

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TitanCNA:Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.

Maintained by Gavin Ha. Last updated 5 months ago.

sequencing wholegenome dnaseq exomeseq statisticalmethod copynumbervariation hiddenmarkovmodel genetics genomicvariation immunooncology 10x-genomics copy-number-variation genome-sequencing hmm tumor-heterogeneity

10.0 match 96 stars 8.47 score 68 scripts

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pathwayPCA:Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) <https://doi.org/10.1093/bioinformatics/btn458>; Chen et al. (2010) <https://doi.org/10.1002/gepi.20532>; and Chen (2011) <https://doi.org/10.2202/1544-6115.1697>.

Maintained by Gabriel Odom. Last updated 5 months ago.

copynumbervariation dnamethylation geneexpression snp transcription geneprediction genesetenrichment genesignaling genetarget genomewideassociation genomicvariation cellbiology epigenetics functionalgenomics genetics lipidomics metabolomics proteomics systemsbiology transcriptomics classification dimensionreduction featureextraction principalcomponent regression survival multiplecomparison pathways

10.0 match 11 stars 7.74 score 42 scripts

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AneuFinder:Analysis of Copy Number Variation in Single-Cell-Sequencing Data

AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.

Maintained by Aaron Taudt. Last updated 5 months ago.

immunooncology software sequencing singlecell copynumbervariation genomicvariation hiddenmarkovmodel wholegenome cpp

10.0 match 17 stars 7.70 score 37 scripts

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signeR:Empirical Bayesian approach to mutational signature discovery

The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.

Maintained by Renan Valieris. Last updated 5 months ago.

genomicvariation somaticmutation statisticalmethod visualization bioconductor bioinformatics openblas cpp

10.0 match 13 stars 7.67 score 22 scripts

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missMethyl:Analysing Illumina HumanMethylation BeadChip Data

Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

Maintained by Belinda Phipson. Last updated 13 days ago.

normalization dnamethylation methylationarray genomicvariation geneticvariability differentialmethylation genesetenrichment

10.0 match 7.24 score 300 scripts 1 dependents

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COCOA:Coordinate Covariation Analysis

COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.

Maintained by John Lawson. Last updated 5 months ago.

epigenetics dnamethylation atacseq dnaseseq methylseq methylationarray principalcomponent genomicvariation generegulation genomeannotation systemsbiology functionalgenomics chipseq sequencing immunooncology dna-methylation pca

10.0 match 10 stars 7.02 score 21 scripts

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SomaticSignatures:Somatic Signatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

Maintained by Julian Gehring. Last updated 5 months ago.

sequencing somaticmutation visualization clustering genomicvariation statisticalmethod

10.0 match 22 stars 6.85 score 54 scripts 1 dependents

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YAPSA:Yet Another Package for Signature Analysis

This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.

Maintained by Zuguang Gu. Last updated 5 months ago.

sequencing dnaseq somaticmutation visualization clustering genomicvariation statisticalmethod biologicalquestion

10.0 match 6.41 score 57 scripts

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kissDE:Retrieves Condition-Specific Variants in RNA-Seq Data

Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data.

Maintained by Aurélie Siberchicot. Last updated 5 months ago.

alternativesplicing differentialsplicing experimentaldesign genomicvariation rnaseq transcriptomics

10.0 match 3 stars 5.98 score 7 scripts

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pgxRpi:R wrapper for Progenetix

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

Maintained by Hangjia Zhao. Last updated 13 days ago.

copynumbervariation genomicvariation dataimport software

10.0 match 3 stars 5.95 score 6 scripts

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MungeSumstats:Standardise summary statistics from GWAS

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

Maintained by Alan Murphy. Last updated 3 months ago.

snp wholegenome genetics comparativegenomics genomewideassociation genomicvariation preprocessing

10.0 match 1 stars 5.87 score 91 scripts

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CNVRanger:Summarization and expression/phenotype association of CNV ranges

The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.

Maintained by Ludwig Geistlinger. Last updated 5 months ago.

copynumbervariation differentialexpression geneexpression genomewideassociation genomicvariation microarray rnaseq snp bioconductor-package u24ca289073

10.0 match 7 stars 5.77 score 12 scripts

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TVTB:TVTB: The VCF Tool Box

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

software genetics geneticvariability genomicvariation datarepresentation gui dnaseq wholegenome visualization multiplecomparison dataimport variantannotation sequencing coverage alignment sequencematching

10.0 match 2 stars 5.76 score 16 scripts

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RIVER:R package for RIVER (RNA-Informed Variant Effect on Regulation)

An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.

Maintained by Yungil Kim. Last updated 5 months ago.

geneexpression geneticvariability snp transcription functionalprediction generegulation genomicvariation biomedicalinformatics functionalgenomics genetics systemsbiology transcriptomics bayesian clustering transcriptomevariant regression functional-variants variant

10.0 match 11 stars 5.52 score 5 scripts

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CrispRVariants:Tools for counting and visualising mutations in a target location

CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.

Maintained by Helen Lindsay. Last updated 5 months ago.

immunooncology crispr genomicvariation variantdetection geneticvariability datarepresentation visualization sequencing

10.0 match 5.51 score 32 scripts

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MouseFM:In-silico methods for genetic finemapping in inbred mice

This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%).

Maintained by Matthias Munz. Last updated 5 months ago.

genetics snp genetarget variantannotation genomicvariation multiplecomparison systemsbiology mathematicalbiology patternlogic geneprediction biomedicalinformatics functionalgenomics finemap gene-candidates inbred-mice inbred-strains mouse qtl qtl-mapping

10.0 match 5.13 score 5 scripts

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semisup:Semi-Supervised Mixture Model

Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.

Maintained by Armin Rauschenberger. Last updated 5 months ago.

snp genomicvariation somaticmutation genetics classification clustering dnaseq microarray multiplecomparison

10.0 match 1 stars 5.08 score 4 scripts

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tadar:Transcriptome Analysis of Differential Allelic Representation

This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.

Maintained by Lachlan Baer. Last updated 2 months ago.

sequencing rnaseq snp genomicvariation variantannotation differentialexpression

10.0 match 1 stars 4.95 score 4 scripts

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scQTLtools:An R package for single-cell eQTL analysis and visualization

This package specializes in analyzing and visualizing eQTL at the single-cell level. It can read gene expression matrices or Seurat data, or SingleCellExperiment object along with genotype data. It offers a function for cis-eQTL analysis to detect eQTL within a given range, and another function to fit models with three methods. Using this package, users can also generate single-cell level visualization result.

Maintained by Xiaofeng Wu. Last updated 2 months ago.

software geneexpression geneticvariability snp differentialexpression genomicvariation variantdetection genetics functionalgenomics systemsbiology regression singlecell normalization visualization rna-seq sc-eqtl

10.0 match 3 stars 4.95 score

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myvariant:Accesses MyVariant.info variant query and annotation services

MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services

Maintained by Adam Mark, Chunlei Wu. Last updated 5 months ago.

variantannotation annotation genomicvariation

10.0 match 4.92 score 28 scripts

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decompTumor2Sig:Decomposition of individual tumors into mutational signatures by signature refitting

Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

Maintained by Rosario M. Piro. Last updated 5 months ago.

software snp sequencing dnaseq genomicvariation somaticmutation biomedicalinformatics genetics biologicalquestion statisticalmethod

10.0 match 1 stars 4.78 score 10 scripts 1 dependents

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transmogR:Modify a set of reference sequences using a set of variants

transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.

Maintained by Stevie Pederson. Last updated 26 days ago.

alignment genomicvariation sequencing transcriptomevariant zlib

10.0 match 4.70 score 2 scripts

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ELViS:An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile

Base-resolution copy number analysis of viral genome. Utilizes base-resolution read depth data over viral genome to find copy number segments with two-dimensional segmentation approach. Provides publish-ready figures, including histograms of read depths, coverage line plots over viral genome annotated with copy number change events and viral genes, and heatmaps showing multiple types of data with integrative clustering of samples.

Maintained by Jin-Young Lee. Last updated 11 days ago.

copynumbervariation coverage genomicvariation biomedicalinformatics sequencing normalization visualization clustering

10.0 match 4.70 score 7 scripts

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scoreInvHap:Get inversion status in predefined regions

scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.

Maintained by Dolors Pelegri-Siso. Last updated 5 months ago.

snp genetics genomicvariation

10.0 match 4.34 score 11 scripts

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CNAnorm:A normalization method for Copy Number Aberration in cancer samples

Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.

Maintained by Stefano Berri. Last updated 5 months ago.

copynumbervariation sequencing coverage normalization wholegenome dnaseq genomicvariation fortran

10.0 match 4.30 score 6 scripts

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gmoviz:Seamless visualization of complex genomic variations in GMOs and edited cell lines

Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.

Maintained by Kathleen Zeglinski. Last updated 5 months ago.

visualization sequencing geneticvariability genomicvariation coverage

10.0 match 4.30 score 9 scripts

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panelcn.mops:CNV detection tool for targeted NGS panel data

CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.

Maintained by Gundula Povysil. Last updated 5 months ago.

sequencing copynumbervariation cellbiology genomicvariation variantdetection genetics

10.0 match 4.08 score 12 scripts

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CINdex:Chromosome Instability Index

The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.

Maintained by Yuriy Gusev. Last updated 5 months ago.

software copynumbervariation genomicvariation acgh microarray genetics sequencing

10.0 match 4.08 score 2 scripts

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GenomicOZone:Delineate outstanding genomic zones of differential gene activity

The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.

Maintained by Hua Zhong. Last updated 5 months ago.

software geneexpression transcription differentialexpression functionalprediction generegulation biomedicalinformatics cellbiology functionalgenomics genetics systemsbiology transcriptomics clustering regression rnaseq annotation visualization sequencing coverage differentialmethylation genomicvariation structuralvariation copynumbervariation

10.0 match 4.00 score

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seqCAT:High Throughput Sequencing Cell Authentication Toolkit

The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.

Maintained by Erik Fasterius. Last updated 5 months ago.

coverage genomicvariation sequencing variantannotation

10.0 match 4.00 score

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geneAttribution:Identification of candidate genes associated with genetic variation

Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.

Maintained by Arthur Wuster. Last updated 5 months ago.

snp geneprediction genomewideassociation variantannotation genomicvariation

10.0 match 4.00 score 3 scripts

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RareVariantVis:A suite for analysis of rare genomic variants in whole genome sequencing data

Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.

Maintained by Tomasz Stokowy. Last updated 5 months ago.

genomicvariation sequencing wholegenome

10.0 match 3.90 score 1 scripts

rli012

Hapi:Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

Inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Maintained by Ruidong Li. Last updated 7 years ago.

snp genomicvariation genetics hiddenmarkovmodel singlecell sequencing microarray

10.0 match 3.79 score 41 scripts

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iGC:An integrated analysis package of Gene expression and Copy number alteration

This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

Maintained by Liang-Bo Wang. Last updated 5 months ago.

software biological question differentialexpression genomicvariation assaydomain copynumbervariation geneexpression researchfield genetics technology microarray sequencing workflowstep multiplecomparison

10.0 match 1 stars 3.78 score 1 scripts

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branchpointer:Prediction of intronic splicing branchpoints

Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.

Maintained by Beth Signal. Last updated 5 months ago.

software genomeannotation genomicvariation motifannotation

10.0 match 3.62 score 21 scripts

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MADSEQ:Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.

Maintained by Yu Kong. Last updated 5 months ago.

genomicvariation somaticmutation variantdetection bayesian copynumbervariation sequencing coverage jags cpp

10.0 match 4 stars 3.60 score 1 scripts

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ipdDb:IPD IMGT/HLA and IPD KIR database for Homo sapiens

All alleles from the IPD IMGT/HLA <https://www.ebi.ac.uk/ipd/imgt/hla/> and IPD KIR <https://www.ebi.ac.uk/ipd/kir/> database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.

Maintained by Steffen Klasberg. Last updated 5 months ago.

genomicvariation sequencematching variantannotation datarepresentation annotationhubsoftware

10.0 match 3.30 score 4 scripts

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cpvSNP:Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.

Maintained by Caitlin McHugh. Last updated 5 months ago.

genetics statisticalmethod pathways genesetenrichment genomicvariation

10.0 match 3.30 score 3 scripts

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RepViz:Replicate oriented Visualization of a genomic region

RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data.

Maintained by Thomas Faux, Asta Laiho. Last updated 5 months ago.

workflowstep visualization sequencing chipseq atacseq software coverage genomicvariation

10.0 match 3.30 score 1 scripts