target - Predict Combined Function of Transcription Factors
Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) <doi: 10.1038/nprot.2013.150>. Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.
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softwarestatisticalmethodtranscriptionalgorithmchip-seqdna-bindinggene-regulationtranscription-factors
8.07 score 5 stars 2.0k scripts 465 downloadssegmenter - Perform Chromatin Segmentation Analysis in R by Calling ChromHMM
Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.
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softwarehistonemodificationbioconductorchromhmmsegmentation-an
4.82 score 6 stars 11 scripts 434 downloadscolocr - Conduct Co-Localization Analysis of Fluorescence Microscopy Images
Automate the co-localization analysis of fluorescence microscopy images. Selecting regions of interest, extract pixel intensities from the image channels and calculate different co-localization statistics. The methods implemented in this package are based on Dunn et al. (2011) <doi:10.1152/ajpcell.00462.2010>.
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colocalizationimage-analysis
4.41 score 26 stars 60 downloadscuratedAdipoArray - A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations
A curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.
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experimentdataexperimenthubgeomicroarraydataadipocyte-differentiationcurated-datamicroarraysperturbationsdatapkg
4.00 scorecuratedAdipoChIP - A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data.
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experimentdataexperimenthubgeochipseqdatasequencingdatadatapkg
4.00 score 1 stars 1 scriptscuratedAdipoRNA - A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.
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experimentdatageornaseqdatasequencingdataadiposernaseqdatapkg
4.00 score 4 scripts