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.
Last updated 24 days ago
softwarestatisticalmethodtranscriptionalgorithmchip-seqdna-bindinggene-regulationtranscription-factors
7.78 score 4 stars 1.3k scripts 192 downloadspcr - Analyzing Real-Time Quantitative PCR Data
Calculates the amplification efficiency and curves from real-time quantitative PCR (Polymerase Chain Reaction) data. Estimates the relative expression from PCR data using the double delta CT and the standard curve methods Livak & Schmittgen (2001) <doi:10.1006/meth.2001.1262>. Tests for statistical significance using two-group tests and linear regression Yuan et al. (2006) <doi: 10.1186/1471-2105-7-85>.
Last updated 4 months ago
data-analysesmolecular-biologyqpcr
7.20 score 26 stars 61 scripts 367 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>.
Last updated 5 years ago
colocalizationimage-analysis
5.76 score 26 stars 22 scripts 135 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.
Last updated 24 days ago
softwarehistonemodificationbioconductorchromhmmsegmentation-an
4.60 score 4 stars 9 scripts 212 downloadscRegulome - Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
Builds a 'SQLite' database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) in cancer from the Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and 'miRCancerdb' databases (in press). Provides custom classes and functions to query, tidy and plot the correlation data.
Last updated 5 years ago
cancer-genomicsdatabasedatasciencemicrornapeer-reviewedtcga-datatranscription-factors
3.69 score 3 stars 54 scripts 61 downloads