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Platform Design Info for Affymetrix Clariom_S_Human.
Platform Design Info for The Manufacturer's Name YG_S98.
Platform Design Info for Affymetrix PorGene-1_0-st.
Platform Design Info for The Manufacturer's Name HG-U133A.
Platform Design Info for The Manufacturer's Name RN_U34.
Platform Design Info for The Manufacturer's Name HG-U133B.
Platform Design Info for Affymetrix HuGene-1_0-st-v1.
Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.
Platform Design Info for Affymetrix CanGene-1_1-st.
Platform Design Info for Affymetrix MTA-1_0.
Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.
Platform Design Info for Affymetrix SoyGene-1_0-st.
Platform Design Info for Affymetrix MedGene-1_0-st.
Platform Design Info for Affymetrix FinGene-1_1-st.
Demultiplexing and filtering utilities intended for reads with combinatorial barcodes (i.e. PETRI-seq and SPLiT-seq). The demultiplexer algorithm uses the position of the segments to extract and compare the barcodes with the reference (whitelist). A Shiny application is provided to interactively select cutoffs for which barcode combinations to keep.
Platform Design Info for Affymetrix MoEx-1_0-st-v1.
Platform Design Info for The Manufacturer's Name Mouse430A_2.
Platform Design Info for Affymetrix CHOGene-2_1-st.
pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.
Platform Design Info for Affymetrix RUSGene-1_1-st.
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.
Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.
Reads files exported from QX Manager or QuantaSoft containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.
Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0).