Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima.

Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.

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

Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects.

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

Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3, 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 (rn4, Nov. 2004) and stored in Biostrings objects.

Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam2, 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 mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects.

Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce11, Feb. 2013) and stored in Biostrings objects.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal6, Mar. 2018) and stored in Biostrings objects.

Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm10, based on GRCm38.p6) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm10, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask).

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

Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro3, 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 reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv2) and available at the URGI (INRA).

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-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.

Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet.

BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments.

iFull genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase (assembly4, Feb. 2008) and stored in Biostrings objects.

This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.

Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects.

This package provides tools to normalize (several) Hi-C data from replicates.