Showing 14 of total 14 results (show query)
openbiox
UCSCXenaShiny:Interactive Analysis of UCSC Xena Data
Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Maintained by Shixiang Wang. Last updated 4 months ago.
cancer-datasetshiny-appsucsc-xena
21.9 match 96 stars 8.54 score 35 scripts
ropensci
UCSCXenaTools:Download and Explore Datasets from UCSC Xena Data Hubs
Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Maintained by Shixiang Wang. Last updated 5 months ago.
api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
11.5 match 106 stars 8.55 score 163 scripts 1 dependents
bioc
singscore:Rank-based single-sample gene set scoring method
A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample's gene expression profile. It scores the expression activities of gene sets at a single-sample level.
Maintained by Malvika Kharbanda. Last updated 5 months ago.
softwaregeneexpressiongenesetenrichmentbioinformatics
6.8 match 41 stars 10.03 score 124 scripts 4 dependentsbioc
MCbiclust:Massive correlating biclusters for gene expression data and associated methods
Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.
Maintained by Robert Bentham. Last updated 5 months ago.
immunooncologyclusteringmicroarraystatisticalmethodsoftwarernaseqgeneexpression
9.8 match 4.00 score 2 scriptsbioc
PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Maintained by Benjamin Haibe-Kains. Last updated 2 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogxcpp
3.4 match 68 stars 11.39 score 442 scripts 3 dependentsbioc
CTdata:Data companion to CTexploreR
Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.
Maintained by Laurent Gatto. Last updated 5 months ago.
transcriptomicsepigeneticsgeneexpressiondataimportexperimenthubsoftware
5.6 match 1 stars 5.69 score 1 scripts 1 dependentsbioc
mastR:Markers Automated Screening Tool in R
mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.
Maintained by Jinjin Chen. Last updated 5 months ago.
softwaregeneexpressiontranscriptomicsdifferentialexpressionvisualization
6.2 match 4 stars 5.08 score 3 scriptsbioc
CaDrA:Candidate Driver Analysis
Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA's main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.
Maintained by Reina Chau. Last updated 5 months ago.
microarrayrnaseqgeneexpressionsoftwarefeatureextraction
3.6 match 24 stars 7.19 score 12 scriptsbioc
CTexploreR:Explores Cancer Testis Genes
The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.
Maintained by Axelle Loriot. Last updated 5 months ago.
transcriptomicsepigeneticsdifferentialexpressiongeneexpressiondnamethylationexperimenthubsoftwaredataimportbioconductor
4.1 match 5.02 score 2 scripts
calvintchi
hierBipartite:Bipartite Graph-Based Hierarchical Clustering
Bipartite graph-based hierarchical clustering performs hierarchical clustering of groups of samples based on association patterns between two sets of variables. It is developed for pharmacogenomic datasets and datasets sharing the same data structure. In the context of pharmacogenomic datasets, the samples are cell lines, and the two sets of variables are typically expression levels and drug sensitivity values. For this method, sparse canonical correlation analysis from Lee, W., Lee, D., Lee, Y. and Pawitan, Y. (2011) <doi:10.2202/1544-6115.1638> is first applied to extract association patterns for each group of samples. Then, a nuclear norm-based dissimilarity measure is used to construct a dissimilarity matrix between groups based on the extracted associations. Finally, hierarchical clustering is applied.
Maintained by Calvin Chi. Last updated 4 years ago.
3.3 match 1 stars 3.70 score 4 scriptsbioc
CRISPRball:Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering
A Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.
Maintained by Jared Andrews. Last updated 3 months ago.
softwareshinyappscrisprqualitycontrolvisualizationguicrispr-screendata-visualizationinteractive-visualizationsmageckplotlyscreeningshiny
1.7 match 9 stars 6.03 score 24 scriptsbioc
Uniquorn:Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
'Uniquorn' enables users to identify cancer cell lines. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file).
Maintained by Raik Otto. Last updated 5 months ago.
immunooncologystatisticalmethodwholegenomeexomeseq
2.3 match 4.30 score
yuting1214
TensorTest2D:Fitting Second-Order Tensor Data
An implementation of fitting generalized linear models on second-order tensor type data. The functions within this package mainly focus on parameter estimation, including parameter coefficients and standard deviation.
Maintained by Mark Chen. Last updated 8 months ago.
3.3 match 1 stars 2.70 score 5 scripts