Platform Design Info for Affymetrix MarGene-1_0-st.

Platform Design Info for The Manufacturer's Name ATH1-121501.

Platform Design Info for Affymetrix Clariom_S_Human_HT.

FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) assembled using data from public repositories.

This package provides a comprehensive set of external and internal evaluation metrics. It includes metrics for assessing partitions or fuzzy partitions derived from clustering results, as well as for evaluating subpopulation identification results within embeddings or graph representations. Additionally, it provides metrics for comparing spatial domain detection results against ground truth labels, and tools for visualizing spatial errors.

Platform Design Info for The Manufacturer's Name HG_U95D.

Platform Design Info for The Manufacturer's Name HC_G110.

Platform Design Info for The Manufacturer's Name Cotton.

Platform Design Info for Affymetrix RabGene-1_0-st.

FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.

This package infers maternal and paternal transmitted and non-transmitted alleles from phased trio genotype data. The package supports SNP-level analyses of genetic nurture and transgenerational effects. It interoperates with Bioconductor VCF infrastructure through support for VariantAnnotation::VCF objects and returns R objects for downstream analysis.

Platform Design Info for The Manufacturer's Name HG-Focus.

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.

Platform Design Info for The Manufacturer's Name HT_HG-U133A.

Platform Design Info for The Manufacturer's Name YG_S98.

This package provides a Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

Platform Design Info for The Manufacturer's Name Yeast_2.

Platform Design Info for The Manufacturer's Name MG_U74Cv2.

Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).

The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.