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Complexome Profiling Analysis package

This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.

Representation of SQL tables in DataFrame metaphor

Implements bindings for SQL tables that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows SQL-derived data to be easily used inside other Bioconductor...

SQLites, tibbles, and data.tables for AnnotationHub

Supplies AnnotationHub with some preprocessed sqlite, tibble, and data.table datasets of PubMed. All the datasets are generated by our Snakemake workflow [pubmed-workflow](https://github.com/rikenbit/pubmed-workflow...

Supplementary data package for Dona et al. (2013) containing example images and tables

...Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics.

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

...The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

Outlier Analysis for pairwise differential comparison

...as phosphoproteomics or transcriptomics, but it can be used for any data that can be represented by a 2D table, and has two sub populations within the table to compare.

Functional annotation-driven unsupervised clustering for single-cell data

...Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign...

Tools for making reports in various formats

...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...

Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data

Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.

Batch Processing and Harmonization of Quantitative Proteomics Table

ProteinBatcher provides utilities to read, validate, and harmonize quantitative proteomics result tables generated by DIA-NN from data-independent acquisition mass spectrometry experiments. The package enables batch processing of multiple...

LinkHD: a versatile framework to explore and integrate heterogeneous data

...Conjointe de Tableaux”), a family of methods to join and compare information from multiple subspaces. However, STATIS-ACT has some drawbacks since it only allows continuous data and it is...

An interface package for the BIOM file format

...This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as...

Mapping of Metabolite IDs from Different Sources

The package provides a comprehensive mapping table of nine different Metabolite ID formats and their common name. The data has been collected and merged from four publicly available source, including...

Graphical Exploration of Design Matrices

Given a sample data table and a design formula, ExploreModelMatrix generates an interactive application for exploration of the resulting design matrix. This can be helpful for interpreting model coefficients and...

Genomic coordinates of problematic genomic regions

...GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC 'gap' table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome...

Preprocessing of FIA-HRMS data

...The peak table can then be exported as a .tsv file for further analysis. Visualisations to assess the quality of the data and of the signal made are easely produced.

Genomic coordinates of problematic genomic regions

...Includes GRanges of various genome gaps, such as centromeres, telomeres, known heterochromatin regions, etc. (UCSC 'gap' table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome...

TSS sequencing data analysis

...Map (BAM) files (single-ended or paired-ended), Browser Extension Data (bed) files, BigWig files, ctss files or tss tables. TSSr also generates various types of TSS or core promoter...

Example DNAm Data for DMRsegal

...Includes a sorted beta matrix as a tab-delimited, bgzip-compressed file and a matching phenotype table. The data contains 10 healthy and 10 cancer samples, and preprocessing has already...

An R package for analysis of massive parallel sequencing based RNA structure probing data

...It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.