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Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome.
Platform Design Info for The Manufacturer's Name HC_G110.
High-throughput omics data are often affected by systematic biases introduced throughout all the steps of a clinical study, from sample collection to quantification. Normalization methods aim to adjust for these biases to make the actual biological signal more prominent. However, selecting an appropriate normalization method is challenging due to the wide range of available approaches. Therefore, a comparative evaluation of unnormalized and normalized data is essential in identifying an appropriate normalization strategy for a specific data set. This R package provides different functions for preprocessing, normalizing, and evaluating different normalization approaches. Furthermore, normalization methods can be evaluated on downstream steps, such as differential expression analysis and statistical enrichment analysis. Spike-in data sets with known ground truth and real-world data sets of biological experiments acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can be analyzed.
Platform Design Info for The Manufacturer's Name Canine_2.
Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.
Platform Design Info for Affymetrix RaGene-2_0-st.
Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177.
This package provides a fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.
Platform Design Info for Affymetrix MTA-1_0.
Store phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata.
Platform Design Info for Affymetrix CyRGene-1_1-st.
Platform Design Info for Affymetrix RUSGene-1_0-st.
Platform Design Info for The Manufacturer's Name Celegans.
preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution. As an input, it takes BED-formatted genomic coordinates of domain boundaries detected from low-resolution Hi-C data, and coordinates of high-resolution genomic annotations from ENCODE or other consortia. preciseTAD employs several feature engineering strategies and resampling techniques to address class imbalance, and trains an optimized random forest model for predicting low-resolution domain boundaries. Translated on a base-level, preciseTAD predicts the probability for each base to be a boundary. Density-based clustering and scalable partitioning techniques are used to detect precise boundary regions and summit points. Compared with low-resolution boundaries, preciseTAD boundaries are highly enriched for CTCF, RAD21, SMC3, and ZNF143 signal and more conserved across cell lines. The pre-trained model can accurately predict boundaries in another cell line using CTCF, RAD21, SMC3, and ZNF143 annotation data for this cell line.
FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.
Platform Design Info for The Manufacturer's Name S_aureus.
Platform Design Info for The Manufacturer's Name Yeast_2.
This package provides a package containing an environment representing the Plasmodium_Anopheles.cdf file.
Platform Design Info for Affymetrix CanGene-1_0-st.
Platform Design Info for Affymetrix BovGene-1_1-st.
Platform Design Info for Affymetrix Mapping250K_Nsp.
Platform Design Info for NimbleGen feinberg_mm8_me_hx1.
Platform Design Info for The Manufacturer's Name RG_U34C.
Platform Design Info for Affymetrix Cytogenetics_Array.