Showing 17 of total 17 results (show query)
tidyverse
ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Maintained by Thomas Lin Pedersen. Last updated 4 days ago.
data-visualisationvisualisation
6.6k stars 25.10 score 645k scripts 7.6k dependents
aphalo
ggpp:Grammar Extensions to 'ggplot2'
Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve; combined stacking and nudging; combined dodging and nudging.
Maintained by Pedro J. Aphalo. Last updated 1 months ago.
data-labelsdatavizggplot2-enhancementsggplot2-geomsggplot2-insetsggplot2-positions
129 stars 12.53 score 582 scripts 26 dependents
bioc
CAMERA:Collection of annotation related methods for mass spectrometry data
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments
Maintained by Steffen Neumann. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
11 stars 10.27 score 175 scripts 6 dependents
kurthornik
NLP:Natural Language Processing Infrastructure
Basic classes and methods for Natural Language Processing.
Maintained by Kurt Hornik. Last updated 4 months ago.
6 stars 9.42 score 1.0k scripts 127 dependents
animint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 1 months ago.
64 stars 8.84 score 173 scriptsbioc
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 3 months ago.
softwareannotationgogenesetenrichmentmultiplecomparisonclusteringvisualization
6.64 score 22 scriptsbioc
SGSeq:Splice event prediction and quantification from RNA-seq data
SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.
Maintained by Leonard Goldstein. Last updated 5 months ago.
alternativesplicingimmunooncologyrnaseqtranscription
5.91 score 45 scripts 3 dependents
cran
ggtern:An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Maintained by Nicholas Hamilton. Last updated 1 years ago.
4 stars 5.09 score 6 dependentsbioc
plyinteractions:Extending tidy verbs to genomic interactions
Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.
Maintained by Jacques Serizay. Last updated 5 months ago.
4.75 score 14 scriptsbioc
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
9 stars 3.95 score 5 scriptsbioc
appreci8R:appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.
Maintained by Sarah Sandmann. Last updated 5 months ago.
variantdetectiongeneticvariabilitysnpvariantannotationsequencing
3.30 score 1 scripts
kasperwelbers
rsyntax:Extract Semantic Relations from Text by Querying and Reshaping Syntax
Various functions for querying and reshaping dependency trees, as for instance created with the 'spacyr' or 'udpipe' packages. This enables the automatic extraction of useful semantic relations from texts, such as quotes (who said what) and clauses (who did what). Method proposed in Van Atteveldt et al. (2017) <doi:10.1017/pan.2016.12>.
Maintained by Kasper Welbers. Last updated 3 years ago.
3.19 score 19 scripts 4 dependents
valcu
annotator:Image Annotation and Polygon Outlining using Free Drawing
Provides functions to create image annotations through polygon outlining. Annotator has the same function as 'graphics::locator()' but achieves its purpose through drawing, rather than multiple mouse clicks. It is based on the 'htmlwidgets' package and 'fabric.js' JavaScript library <http://fabricjs.com/>.
Maintained by Mihai Valcu. Last updated 1 years ago.
3 stars 3.18 score 4 scripts
daniel-jg
IntervalSurgeon:Operating on Integer-Bounded Intervals
Manipulate integer-bounded intervals including finding overlaps, piling and merging.
Maintained by Daniel Greene. Last updated 1 years ago.
2.73 score 18 scripts 1 dependents
cmerow
maskRangeR:Mask Species Geographic Ranges
Mask ranges based on expert knowledge or remote sensing layers. These tools can be combined to quantitatively and reproducibly generate a new map or to update an existing map. Methods include expert opinion and data-driven tools to generate thresholds for binary masks.
Maintained by Cory Merow. Last updated 3 years ago.
2.48 score 6 scriptscran
SNPannotator:Investigating the Functional Characteristics of Selected SNPs and Their Vicinity Genomic Region
To investigate the functional characteristics of selected SNPs and their vicinity genomic region. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Maintained by Alireza Ani. Last updated 2 years ago.
1.00 score