This package provides a package containing an environment representing the Hu35KsubC.CDF file.

This package provides a package containing an environment representing the HT_HG-U133B.cdf file.

This package provides a package containing an environment representing the HT_MG-430A.cdf file.

This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering".

This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881.".

Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster) assembled using data from public repositories.

Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k) assembled using data from public repositories.

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b) assembled using data from public repositories.

This package provides a package containing an environment representing the HG_U95E.CDF file.

Affymetrix Affymetrix Hu35KsubD Array annotation data (chip hu35ksubd) assembled using data from public repositories.

Dataset package containing gene and isoform count matrices, and sample metadata for long-read direct cDNA sequencing of human retinal organoids, 2D retinal ganglion cell (RGC) cultures, and flowthrough fractions from H9 and EP1 iPSC cell lines. Data were generated using Oxford Nanopore Technology (ONT) direct cDNA sequencing and mapped to the GRCh38 reference genome (GENCODE v46 annotation). The package provides accessor functions returning SummarizedExperiment objects for gene-level counts, isoform-level counts, and a matrix of allele-specific expression (ASE) gene counts. Data files are stored in flat CSV format in an Open Science Framework (OSF) repository and cached locally via BiocFileCache.

Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) assembled using data from public repositories.

Affymetrix hta20 annotation data (chip hta20transcriptcluster) assembled using data from public repositories.

This package provides a package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.

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 HT\_MG-430\_PM\_probe\_tab.

This package provides a package containing an environment representing the Hu6800subA.CDF file.

An interactive tool to visualize long vectors of integer data by means of Hilbert curves.

This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.

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 HT\_MG-430B\_probe\_tab.

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 HT\_HG-U133\_Plus\_PM\_probe\_tab.

Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip hthgu133plusa) assembled using data from public repositories.

Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus) assembled using data from public repositories.

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 Hu35KsubD\_probe\_tab.