Samples (-omics, imaging, single cell, etc) often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.

Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects.

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn4, 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.

Full genome sequences for Macaca fascicularis (Crab-eating macaque) as provided by NCBI (assembly Macaca_fascicularis_6.0, assembly accession GCA_011100615.1) and stored in Biostrings objects.

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

Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.

This package implements a variety of methods for batch correction in single-cell RNA sequencing (scRNA-seq) data. It incorporates quantitative metrics (e.g. Wasserstein distance, Adjusted Rand Index) to evaluate their performance. Furthermore, the package assists users in identifying and applying the optimal method for specific datasets.

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

Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects.

Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

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

This package provides a much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.

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

This package provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries.

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro5, May 2016) and stored in Biostrings objects.

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings objects. Only single nucleotide variants (SNVs) were considered. At each SNV, the most frequent allele was chosen at the major allele to be injected into the reference genome.

Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan2, Dec. 2015) and stored in Biostrings objects.

Parse GFF and GTF files using C++ classes. The package also provides utilities to read and write GFF3 files. The GFF (General Feature Format) format is a tab-delimited file format for describing genes and other features of DNA, RNA, and protein sequences. GFF files are often used to describe the features of genomes.

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.

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn6, Jul. 2014) and stored in Biostrings objects.

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Only common single nucleotide variants (SNVs) with at least one alternate allele with frequency greater than 0.01 were considered. For SNVs with more than 1 alternate allele, the most frequent allele was chosen as the minor allele to be injected into the reference genome.

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (genome rn7) and stored in Biostrings objects.

This package allows interactive viewing of package maintainer information. The Bioconductor Package Maintainer Application sends yearly verification emails to accept Bioconductor policies; this application also depicts maintainer status on opting in and if the email is deemed valid.