Question: Recent changes to Bioconductor packages
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gravatar for madman@jimmy.harvard.edu
15.4 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 04 March 2004: PROcess: Added new package. JG 04 March 2004: Ruuid - Modified the .Call() calls to meet current standards. JG 04 March 2004: limma 1.5.3. - new function smoothVar() - source="agilent" added to read.maimages - bug fixed in heatdiagram() and heatDiagram() which caused over- printing when using par(mfrow) - vennCounts() now uses table() for major computation and is therefore much faster - new function FStat() - S3 class "classification" replaced by S4 class "TestResults", including 'show' and 'summary' methods - classifyTests(), classifyTestsT() and classifyTestsP() now produce "TestResults" objects 02 March 2004: annotae - getDOdesc modified in response to changes in the GO data pacakge. The argument "which" can be MF, CC, BP, or ANY. JZ 02 March 2004: graph - Added a set of coersion functions & methods to convert various forms of matrices into graphs. An adjacency matrix can be directly converted to a garph using 'as', and the functions 'aM2bpG' and 'ftM2adjM' have been added as well. JG 02 March 2004: EBarrays - Added a new contributed package, EBarrays, which provides tools for the analysis of replicated microarray data across multiple conditions. JG
ADD COMMENTlink modified 15.3 years ago • written 15.4 years ago by madman@jimmy.harvard.edu850
Answer: Recent changes to Bioconductor packages
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gravatar for madman@jimmy.harvard.edu
15.4 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 12 Mar 2004: limma 1.5.6. GKS - tetragamma() changed to psigamma(x,deriv=2) with R version check - bug fix to normalizeRobustSpline() to prevent error when spline basis becomes singular - La.eigen() to eigen() in is.fullrank() 12 Mar 2004: convert 1.1. GKS New package for converting between microarray data classes. 10 Mar 2004: ecoliLeucine - moved it over to experimental data. JG 10 Mar 2004: experimental data - there is now a reposTools style repository for experimental data. JG 10 Mar 2004: reposTools - added an option to 'repositories2' to automatically detect the BioC experimental data repository. JG 10 Mar 2004: several packages - removed the use of 'multiget' in favor of 'mget'. JG Mra 9, 2003: metaData - New versions of annotation are available for downloading from the seb site. NULL values in the GO environment have been replaced by NA. JZ 8 Mar 2004: limma 1.5.4. GKS Now passes R CMD check in R 1.9.0dev. - new argument 'mar' for vennDiagram(), reduces white-space for venn Diagrams - new argument 'annotation' for read.maimages() - fix bug in gls.series to ensure that spacing and weights arguments are passed to duplicateCorrelation() - check for R version when setting package argument for .C and .Fortran calls
ADD COMMENTlink written 15.4 years ago by madman@jimmy.harvard.edu850
Answer: Recent changes to Bioconductor packages
0
gravatar for madman@jimmy.harvard.edu
15.4 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 19 Mar 2004: affy 1.4.21 (this reports changes that happened during the very last versions). LG - the pack needs R-1.9.0-to-be-released (a fairly recent R-devel is enough). - the deprecated option 'xy' in indexProbes (and friends) was removed. - the xy coordinates starting at one (but not at zero) complication has been sorted out (package-wide option introduced as a global switch) - fixed issue with computeExprSet when querying unknown affyids (no longer crashes). - better handling or errors when running computeExprSet 17 Mar 2004: altcdfenvs - A package to help building alternative associations between identifiers and probes on microarrays. The code and examples apply directly to Affymetrix data. The vignette provides a step-by-step tutorial to go from a given set of reference sequences in a FASTA file to a cdfenv to be used with AffyBatch objects. LG 16 Mar 2004: limma 1.5.7. GKS - Sweave-style vignette added, as well as User's Guide - new function array2channel() to convert targets files from by-array to by-channel representation - removed warning about Cy3, Cy5 columns from readTargets() - more general use of 'ref' in modelMatrix(), doesn't have to occur on every array - target names are sorted in modelMatrix() - designMatrix() renamed to modelMatrix(), designMatrix() deprecated - new function lmsc.series() for single-channel linear models 15 Mar 2004: Biobase - modified the openVignette code to use the new .rds metafiles instead of the 00Index files. JG
ADD COMMENTlink written 15.4 years ago by madman@jimmy.harvard.edu850
Answer: Recent changes to Bioconductor packages
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gravatar for madman@jimmy.harvard.edu
15.3 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only.
ADD COMMENTlink written 15.3 years ago by madman@jimmy.harvard.edu850
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