This package provides a database of PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137.

This package efficiently obtains count vectors from indexed bam files. It counts the number of nucleotide sequence reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

This package provides tools for large-scale identification and advanced visualization of sets of conserved noncoding elements.

The package provides functions to create and use transcript-centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package also provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of K and can reject the null hypothesis K=1.

Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The ggcyto wrapper and some custom layers also make it easy to add gates and population statistics to the plot.

This package provides tools for representing and modeling data in the EMBL-EBI GWAS catalog.

This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.

This package provides a package containing an environment representing the HG_U95Av2.CDF file.

This package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

The package uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

This package provides negative binomial models for two-group comparisons and regression inferences from RNA-sequencing data.

This package provides platform design info for Affymetrix Mapping50K_Xba240 (pd.mapping50k.xba240).

This package is an automatically generated RnBeads annotation package for the assembly hg19.

r-kegggraph is an interface between Kegg Pathway database and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated kgml (Kegg XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.

This package provides an R interface to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects.

The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files.

This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.

This package provides genome wide annotation for E coli strain K12, primarily based on mapping using Entrez Gene identifiers. Entrez Gene is National Center for Biotechnology Information (NCBI)’s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis.

This is a package for biclustering analysis and exploration of results.

This is an R package for doublet annotation of single cell RNA sequencing data. scds provides methods to annotate doublets in scRNA-seq data computationally.