Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.
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GET /api/packages?search=hello&page=1&limit=20
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If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.
The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.
This package provides a Bioconductor data package for the Stockholm dataset.
Platform Design Info for The Manufacturer's Name wheat.
Platform Design Info for Affymetrix MedGene-1_0-st.
PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.
Store phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata.
Platform Design Info for Affymetrix RJpGene-1_0-st.
The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.
Platform Design Info for Affymetrix EquGene-1_0-st.
Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package.
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.
FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) assembled using data from public repositories.
The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.
An experimentdata package to supplement the preciseTAD package containing pre-trained models and the variable importances of each genomic annotation used to build the model parsed into list objects and available in ExperimentHub. In total, preciseTADhub provides access to n=84 random forest classification models optimized to predict TAD/chromatin loop boundary regions and stored as .RDS files. The value, n, comes from the fact that we considered l=2 cell lines GM12878, K562, g=2 ground truth boundaries Arrowhead, Peakachu, and c=21 autosomal chromosomes CHR1, CHR2, ..., CHR22 (omitting CHR9). Furthermore, each object is itself a two-item list containing: (1) the model object, and (2) the variable importances for CTCF, RAD21, SMC3, and ZNF143 used to predict boundary regions. Each model is trained via a "holdout" strategy, in which data from chromosomes CHR1, CHR2, ..., CHRi-1, CHRi+1, ..., CHR22 were used to build the model and the ith chromosome was reserved for testing. See https://doi.org/10.1101/2020.09.03.282186 for more detail on the model building strategy.
PathMED is a collection of tools to facilitate precision medicine studies with omics data (e.g. transcriptomics). Among its funcionalities, genesets scores for individual samples may be calculated with several methods. These scores may be used to train machine learning models and to predict clinical features on new data. For this, several machine learning methods are evaluated in order to select the best method based on internal validation and to tune the hyperparameters. Performance metrics and a ready-to-use model to predict the outcomes for new patients are returned.
Platform Design Info for Affymetrix HuGene-1_0-st-v1.
Platform Design Info for The Manufacturer's Name RG_U34B.
Platform Design Info for Affymetrix CanGene-1_1-st.
Platform Design Info for The Manufacturer's Name Mu11KsubB.
FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories.
Platform Design Info for The Manufacturer's Name HT_MG-430A.
Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles.
Platform Design Info for The Manufacturer's Name HC_G110.
Platform Design Info for The Manufacturer's Name Chicken.