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Platform Design Info for Affymetrix RUSGene-1_0-st.
Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.
Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.
pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.
Platform Design Info for Affymetrix MTA-1_0.
Platform Design Info for Affymetrix CHOGene-2_0-st.
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)).
Platform Design Info for Affymetrix EleGene-1_1-st.
Platform Design Info for The Manufacturer's Name HG-U133A_tag.
Platform Design Info for Affymetrix FelGene-1_1-st.
Platform Design Info for Affymetrix RJpGene-1_0-st.
Platform Design Info for Affymetrix RaGene-1_1-st-v1.
An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.
Platform Design Info for The Manufacturer's Name Celegans.
This package provides a package containing an environment representing the Porcine.cdf file.
This package provides a function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.
It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.
Platform Design Info for The Manufacturer's Name Yeast_2.
PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them.
Platform Design Info for NimbleGen feinberg_mm8_me_hx1.
Platform Design Info for The Manufacturer's Name RG_U34A.
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-Focus.
Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.