You are here

Bioconductor

Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. [Source: Wikipedia ]

cellHTS

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

RNA interference (RNAi) screening is a powerful technology for functional characterization of biological pathways. Interpretation of RNAi screens requires computational and statistical analysis techniques. We describe a method that integrates all steps to generate a scored phenotype list from raw data. It is implemented in an open-source Bioconductor/R package, cellHTS (http://www.dkfz.de/signaling/cellHTS). The method is useful for the analysis and documentation of individual RNAi screens.

Rating: 
Average: 5 (1 vote)

RNAither

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We present RNAither, a package for the free statistical environment R which performs an analysis of high-throughput RNA interference (RNAi) knock-down experiments, generating lists of relevant genes and pathways out of raw experimental data. The library provides a quality assessment of the signal intensities, as well as a broad range of options for data normalization, different statistical tests for the identification of significant siRNAs, and a significance analysis of the biological processes involving corresponding genes.

Rating: 
Average: 5 (1 vote)

AgiMicroRna

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The main research tool for identifying microRNAs involved in specific cellular processes is gene expression profiling using microarray technology. Agilent is one of the major producers of microRNA arrays, and microarray data are commonly analyzed by using R and the functions and packages collected in the Bioconductor project. However, an analytical package that integrates the specific characteristics of microRNA Agilent arrays has been lacking.

Rating: 
Average: 5 (1 vote)

TargetScore

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Systematic identification of microRNA (miRNA) targets remains a challenge. The miRNA overexpression coupled with genome-wide expression profiling is a promising new approach and calls for a new method that integrates expression and sequence information.

Rating: 
Average: 5 (1 vote)

Mirsynergy

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Identification of microRNA regulatory modules (MiRMs) will aid deciphering aberrant transcriptional regulatory network in cancer but is computationally challenging. Existing methods are stochastic or require a fixed number of regulatory modules.

Rating: 
Average: 5 (1 vote)

mdgsa

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Functional interpretation of miRNA expression data is currently done in a three step procedure: select differentially expressed miRNAs, find their target genes, and carry out gene set overrepresentation analysis Nevertheless, major limitations of this approach have already been described at the gene level, while some newer arise in the miRNA scenario.Here, we propose an enhanced methodology that builds on the well-established gene set analysis paradigm.

Rating: 
5
Average: 5 (2 votes)

miRLAB

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

microRNAs (miRNAs) are important gene regulators at post-transcriptional level, and inferring miRNA-mRNA regulatory relationships is a crucial problem. Consequently, several computational methods of predicting miRNA targets have been proposed using expression data with or without sequence based miRNA target information. A typical procedure for applying and evaluating such a method is i) collecting matched miRNA and mRNA expression profiles in a specific condition, e.g.

Rating: 
Average: 5 (1 vote)

ProMISe

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Aberrant microRNA (miRNA) expression is implicated in tumorigenesis. The underlying mechanisms are unclear because the regulations of each miRNA on potentially hundreds of mRNAs are sample specific. We describe a novel approach to inferProbabilisticMiRNA-mRNA Interaction Signature ('ProMISe') from a single pair of miRNA-mRNA expression profile. Our model considers mRNA and miRNA competition as a probabilistic function of the expressed seeds (matches). To demonstrate ProMISe, we extensively exploited The Cancer Genome Atlasdata.

Rating: 
Average: 5 (1 vote)

SpidermiR

Submitted by ChenLiang on Sun, 09/10/2017 - 20:15

Gene Regulatory Networks (GRNs) control many biological systems, but how such network coordination is shaped is still unknown. GRNs can be subdivided into basic connections that describe how the network members interact e.g., co-expression, physical interaction, co-localization, genetic influence, pathways, and shared protein domains. The important regulatory mechanisms of these networks involve miRNAs.

Rating: 
Average: 5 (1 vote)

microRNAome

Submitted by ChenLiang on Tue, 01/09/2018 - 17:31

MicroRNAs are short RNAs that serve as regulators of gene expression and are essential components of normal development as well as modulators of disease. MicroRNAs generally act cell-autonomously, and thus their localization to specific cell types is needed to guide our understanding of microRNA activity. Current tissue-level data have caused considerable confusion, and comprehensive cell-level data do not yet exist. Here, we establish the landscape of human cell-specific microRNA expression.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to Bioconductor