KEGGgraph - KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

Last updated 24 days ago

pathwaysgraphandnetworkvisualizationkegg

9.10 score 26 packages 110 scripts 7.3k downloads

BioQC - Detect tissue heterogeneity in expression profiles with gene sets

BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.

Last updated 24 days ago

geneexpressionqualitycontrolstatisticalmethodgenesetenrichment

7.31 score 5 stars 85 scripts 375 downloads

RTCA - Open-source toolkit to analyse data from xCELLigence System (RTCA)

Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.

Last updated 24 days ago

immunooncologycellbasedassaysinfrastructurevisualizationtimecourse

4.60 score 4 scripts 245 downloads

rqubic - Qualitative biclustering algorithm for expression data analysis in R

This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.

Last updated 24 days ago

clustering

3.78 score 1 packages 4 scripts 270 downloads

ddCt - The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

Last updated 24 days ago

geneexpressiondifferentialexpressionmicrotitreplateassayqpcr

3.78 score 8 scripts 286 downloads