Tools   Select Another Resource Report Type

https://bioconductor.org/packages/2.11/bioc/html/flowPhyto.html

An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

Proper citation: flowPhyto (RRID:SCR_002183) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/MethylAid.html

Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

Proper citation: MethylAid (RRID:SCR_002659) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/wateRmelon.html

Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

Proper citation: wateRmelon (RRID:SCR_001296) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/bioc/spotSegmentation/

Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three.

Proper citation: spotSegmentation (RRID:SCR_001298) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/oneChannelGUI.html

Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.

Proper citation: oneChannelGUI (RRID:SCR_001325) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/affylmGUI/

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

Proper citation: affylmGUI (RRID:SCR_001320) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/arrayQuality.html

Software functions for performing print-run and array level quality assessment.

Proper citation: arrayQuality (RRID:SCR_001315) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/ArrayTools.html

Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

Proper citation: ArrayTools (RRID:SCR_001313) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/affyPLM.html

Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.

Proper citation: affyPLM (RRID:SCR_001319) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/Harshlight.html

Software package used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection.

Proper citation: Harshlight (RRID:SCR_001340) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMetrics.html

Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported.

Proper citation: arrayQualityMetrics (RRID:SCR_001335) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MANOR.html

Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.

Proper citation: MANOR (RRID:SCR_001305) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/dyebias.html

Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.

Proper citation: dyebias (RRID:SCR_001308) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/limmaGUI.html

Software package for a Graphical User Interface for the limma Microarray package.

Proper citation: limmaGUI (RRID:SCR_001306) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ffpe.html

Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Proper citation: ffpe (RRID:SCR_001307) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/SNAGEE.html

Software package that uses signal-to-noise ratios (SNRs) as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.

Proper citation: SNAGEE (RRID:SCR_001301) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/pvac.html

Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

Proper citation: pvac (RRID:SCR_000359) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/OLINgui.html

Software package providing a graphical user interface for the OLIN package.

Proper citation: OLINgui (RRID:SCR_000435) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/Basic4Cseq.html

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Proper citation: Basic4Cseq (RRID:SCR_002836) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/unifiedWMWqPCR.html

Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

Proper citation: unifiedWMWqPCR (RRID:SCR_001706) Copy   

•   Source: SciCrunch Registry