Showing 200 of total 1156 results (show query)

bioc

annotate:Annotation for microarrays

Using R enviroments for annotation.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotationpathwaysgo

97.4 match 11.41 score 812 scripts 243 dependents

kurthornik

NLP:Natural Language Processing Infrastructure

Basic classes and methods for Natural Language Processing.

Maintained by Kurt Hornik. Last updated 4 months ago.

34.3 match 6 stars 9.37 score 1.0k scripts 127 dependents

bioc

Category:Category Analysis

A collection of tools for performing category (gene set enrichment) analysis.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotationgopathwaysgenesetenrichment

26.3 match 7.93 score 183 scripts 16 dependents

bioc

ViSEAGO:ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.

Maintained by Aurelien Brionne. Last updated 2 months ago.

softwareannotationgogenesetenrichmentmultiplecomparisonclusteringvisualization

22.7 match 6.64 score 22 scripts

david-barnett

microViz:Microbiome Data Analysis and Visualization

Microbiome data visualization and statistics tools built upon phyloseq.

Maintained by David Barnett. Last updated 3 months ago.

microbiomemicrobiome-analysismicrobiota

20.6 match 114 stars 6.22 score 480 scripts

bioc

Biobase:Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructurebioconductor-packagecore-package

7.3 match 9 stars 16.45 score 6.6k scripts 1.8k dependents

bioc

geneXtendeR:Optimized Functional Annotation Of ChIP-seq Data

geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

Maintained by Bohdan Khomtchouk. Last updated 5 months ago.

chipseqgeneticsannotationgenomeannotationdifferentialpeakcallingcoveragepeakdetectionchiponchiphistonemodificationdataimportnaturallanguageprocessingvisualizationgosoftwarebioconductorbioinformaticscchip-seqcomputational-biologyepigeneticsfunctional-annotation

30.2 match 9 stars 3.95 score 5 scripts

bioc

BiocGenerics:S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

Maintained by Hervรฉ Pagรจs. Last updated 1 months ago.

infrastructurebioconductor-packagecore-package

8.0 match 12 stars 14.22 score 612 scripts 2.2k dependents

davidgohel

ggiraph:Make 'ggplot2' Graphics Interactive

Create interactive 'ggplot2' graphics using 'htmlwidgets'.

Maintained by David Gohel. Last updated 3 months ago.

libpngcpp

7.5 match 819 stars 14.39 score 4.1k scripts 34 dependents

bioc

SCANVIS:SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).

Maintained by Phaedra Agius. Last updated 5 months ago.

softwareresearchfieldtranscriptomicsworkflowstepannotationvisualization

24.1 match 4.00 score 2 scripts

eltebioinformatics

mulea:Enrichment Analysis Using Multiple Ontologies and False Discovery Rate

Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.

Maintained by Tamas Stirling. Last updated 3 months ago.

annotationdifferentialexpressiongeneexpressiongenesetenrichmentgographandnetworkmultiplecomparisonpathwaysreactomesoftwaretranscriptionvisualizationenrichmentenrichment-analysisfunctional-enrichment-analysisgene-set-enrichmentontologiestranscriptomicscpp

10.0 match 28 stars 7.36 score 34 scripts