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Lengths of mRNA transcripts for a number of genomes

Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser. Data objects are provided as individual pieces of information to be...

Interactive web application for Omics-data analysis

...and/or metabolomics data. The interface offers a guided experience for the user, from the definition of the experimental design to the integration of several omics table together. A report...

Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts

...A PAC object in its most basic form is a list containing three types of data frames. - Phenotype table (P): Sample names (rows) with associated metadata (columns) e.g. treatment...

Single-cell RNAseq cell cluster labelling by reference

...It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).

Illustration of FHIR ingestion and transformation using R

...parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

Extract SBML's data into dataframes

Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i...

Interactive SummarizedExperiment Explorer

...user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive...

Representation of Sparse Experiments and Assays Across Samples

...The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class...

A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata

...for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R.

Quality Control of Protemics Data

...and reproducibility of your proteomics mass spectrometry analysis from MaxQuant.Input data are extracted from several MaxQuant output tables and produces a pdf report. It includes several visualization tools to...

A k-tables approach to integrate multiple Omics-Data

...mixed omics data (transcriptomics, proteomics, microarray-chips, rna-seq data), introducing the following improvements: distance options (for numeric and/or categorical variables) for each of the tables, bootstrap resampling techniques...

Independent Hypothesis Weighting

...method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can...

Data for the HelloRanges tutorial vignette

Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano...

An R Package for retrieving data from DAVID into R objects using Web Services API.

Tools for retrieving data from the Database for Annotation, Visualization and Integrated Discovery (DAVID) using Web Services into R objects. This package offers the main functionalities of DAVID website including...

Data for the ELMER package

...It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth...

Set Based Visualizations for Next-Gen Sequencing Data

...seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

A Shiny App For Visualizing Nanostring GeoMx DSP Data

This package is a Shiny app for interactively analyzing and visualizing Nanostring GeoMX Whole Transcriptome Atlas data. Users have the option of exploring a sample data to explore this app...

Supporting datasets for SBGNview package

...ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage...

Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes

...The purpose of the HPAStainR function is to query the visual staining data in the Human Protein Atlas to return a table of staining ranked cell types. The function also...

R Interface with InterMine-Powered Databases

...It makes most from the correspondence of the data frame object in R and the table object in databases, while hiding the details of data exchange through XML or JSON.