R-universe search: needs:ggbio

Showing 16 of total 16 results (show query)

bioc

FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

Maintained by Changqing Wang. Last updated 2 days ago.

rnaseq singlecell transcriptomics dataimport differentialsplicing alternativesplicing geneexpression longread zlib curl bzip2 xz-utils cpp

33 stars 8.04 score 12 scripts

bioc

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

22 stars 6.85 score 54 scripts 1 dependents

bioc

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

6.41 score 57 scripts

bioc

ReportingTools:Tools for making reports in various formats

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.

Maintained by Jason A. Hackney. Last updated 5 months ago.

immunooncology software visualization microarray rnaseq go datarepresentation genesetenrichment

6.23 score 93 scripts 1 dependents

bioc

scruff:Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.

Maintained by Zhe Wang. Last updated 5 months ago.

software technology sequencing alignment rnaseq singlecell workflowstep preprocessing qualitycontrol visualization immunooncology bioinformatics scrna-seq single-cell umi

8 stars 6.20 score 22 scripts

bioc

affycoretools:Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

Maintained by James W. MacDonald. Last updated 5 months ago.

reportwriting microarray onechannel geneexpression

6.07 score 117 scripts

bioc

R3CPET:3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.

Maintained by Mohamed Nadhir Djekidel. Last updated 5 months ago.

networkinference geneprediction bayesian graphandnetwork network geneexpression hic chia-pet chromatin-interaction dirichlet-process-mixtures transcription-facto cpp

4 stars 5.45 score 5 scripts

bioc

Damsel:Damsel: an end to end analysis of DamID

Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.

Maintained by Caitlin Page. Last updated 5 months ago.

differentialmethylation peakdetection geneprediction genesetenrichment

5.20 score 20 scripts

bioc

derfinderPlot:Plotting functions for derfinder

This package provides plotting functions for results from the derfinder package. This helps separate the graphical dependencies required for making these plots from the core functionality of derfinder.

Maintained by Leonardo Collado-Torres. Last updated 4 months ago.

differentialexpression sequencing rnaseq software visualization immunooncology bioconductor derfinder

2 stars 5.00 score 5 scripts

bioc

msgbsR:msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Pipeline for the anaysis of a MS-GBS experiment.

Maintained by Benjamin Mayne. Last updated 5 months ago.

immunooncology differentialmethylation dataimport epigenetics methylseq

4.48 score 1 scripts

bioc

intansv:Integrative analysis of structural variations

This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.

Maintained by Wen Yao. Last updated 5 months ago.

genetics annotation sequencing software

4.48 score 2 scripts

bioc

cageminer:Candidate Gene Miner

This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.

Maintained by Fabrício Almeida-Silva. Last updated 5 months ago.

software snp functionalprediction genomewideassociation geneexpression networkenrichment variantannotation functionalgenomics network

1 stars 4.30 score 5 scripts

bioc

RiboProfiling:Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

Maintained by A. Popa. Last updated 5 months ago.

riboseq sequencing coverage alignment qualitycontrol software principalcomponent

4.30 score 10 scripts

bioc

CAFE:Chromosmal Aberrations Finder in Expression data

Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input

Maintained by Sander Bollen. Last updated 5 months ago.

geneexpression microarray onechannel genesetenrichment

4.30 score 2 scripts

bioc

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

4.00 score

bioc

BOBaFIT:Refitting diploid region profiles using a clustering procedure

This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.

Maintained by Gaia Mazzocchetti. Last updated 5 months ago.

copynumbervariation clustering visualization normalization software

3.90 score 3 scripts