Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such 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.

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects.

bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations.

Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from samples assayed by Lauren Middleton et. al. (2021).

Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer2, June 2008) and stored in Biostrings objects.

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac3, Mar. 2009) and stored in Biostrings objects.

Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm8, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bovine\_probe\_tab.

Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects.

Battlefield is a Swiss-army toolkit originally developed to define and extract spatial spots from specific tissue regions—such as front regions, niche borders, invasive margins, and cluster interfaces—using spatial transcriptomics data or clustered tissue maps. It has since been extended to support trajectory selection and layer inspection, and now provides a collection of low-level utilities for spatial transcriptomics analysis. These utilities are primarily intended to be reused within higher-level analytical packages. It is designed to work with sequencing-based platforms such as Visium at several resolutions and Visium HD(binned).

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.

The package provides a bioimage dataset for the image analysis using machine learning and deep learning. The dataset includes microscopy imaging data with supervised labels. The data is provided as R list data that can be loaded to Keras/tensorflow in R.

Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.

This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).

The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.1101/525709v2 and https://pubmed.ncbi.nlm.nih.gov/33624743/, the results of module repertoire analyses can be represented in a fingerprint format, where red and blue spots indicate increases or decreases in module activity. These spots are subsequently represented either on a grid, with each position being assigned to a given module, or in a heatmap where the samples are arranged in columns and the modules in rows.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau9, Apr. 2018) and stored in Biostrings objects.

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects.

The barbieQ package provides a series of robust statistical tools for analysing barcode count data generated from cell clonal tracking (i.e., lineage tracing) experiments. In these experiments, an initial cell and its offspring collectively form a clone (i.e., lineage). A unique barcode sequence, incorporated into the DNA of the inital cell, is inherited within the clone. This one-to-one mapping of barcodes to clones enables clonal tracking of their behaviors. By counting barcodes, researchers can quantify the population abundance of individual clones under specific experimental perturbations. barbieQ supports barcode count data preprocessing, statistical testing, and visualization.

This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.

Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object.

Model-based analysis of single-cell methylation data.

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.