Bioconductor Changelog
   


About
Click here to learn more about this blog.


Packages
Click on a link
for updates to that package only.
ABarray
ACME
AffyCompatible
AffyExpress
AffyTiling
Agi4x44PreProcess
AnnBuilder
AnnotationDbi
ArrayExpress
ArrayTools
BAC
BCRANK
BGmix
BSgenome
BUS
BicARE
BioMVCClass
Biobase
BiocCaseStudies
Biostrings
BiostringsCinterfaceDemo
BufferedMatrix
BufferedMatrixMethods
CALIB
CAMERA
CGHbase
CGHcall
CGHregions
CMA
CNTools
CORREP
Category
ChemmineR
CoCiteStats
DAVIDQuery
DEDS
DFP
DNAcopy
DynDoc
EBImage
EBarrays
GEOmetadb
GEOquery
GGBase
GGexplorer
GGtools
GLAD
GOSemSim
GOstats
GSEABase
GSEAlm
GeneMeta
GeneR
GeneRegionScan
GeneRfold
GeneSelectMMD
GeneSelector
GeneSpring
GeneTraffic
GeneticsBase
GeneticsDesign
GeneticsPed
GenomeGraphs
GlobalAncova
GraphAT
GraphAlignment
HELP
HEM
Harshlight
Heatplus
HilbertCurveDisplay
HilbertVis
HilbertVisGUI
IRanges
ITALICS
Icens
KCsmart
KEGGSOAP
KEGGgraph
LBE
LMGene
LPE
LPEadj
MANOR
MCRestimate
MEDME
MLInterfaces
MVCClass
MantelCorr
MassSpecWavelet
MeasurementError.cor
MergeMaid
Mfuzz
MiPP
OCplus
OLIN
OLINgui
OrderedList
OutlierD
PAnnBuilder
PCpheno
PGSEA
PLPE
PROcess
RBGL
RBioinf
RDocBook
RLMM
RMAGEML
RNAither
ROC
RSNPper
RWebServices
RankProd
Ratlpow
RbcBook1
Rdbi
RdbiPgSQL
Rdisop
RefPlus
Resourcerer
Rgraphviz
Ringo
Rintact
Rmagpie
RmiR
RpsiXML
Rredland
Rrsat
Rswub
Rtreemix
Ruuid
SAGElyzer
SAGx
SBMLR
SIM
SJava
SLGI
SLqPCR
SMAP
SNPchip
SPIA
SSPA
ScISI
SemSim
ShortRead
TargetSearch
TypeInfo
VanillaICE
XDE
aCGH
adSplit
affxparser
affy
affyContam
affyExonMuncher
affyMvout
affyPLM
affyPara
affyQCReport
affycomp
affycoretools
affyio
affylmGUI
affypdnn
altcdfenvs
annaffy
annotate
annotationTools
apComplex
aroma.light
aroma.tcga
arrayMagic
arrayMvout
arrayQuality
arrayQualityMetrics
beadarray
beadarraySNP
betr
bgafun
bgx
bioDist
biocDatasets
biocGraph
biocSurvey
biocViews
biomaRt
bridge
buildBioC
caFlowQ
cellHTS
cellHTS2
cghMCR
chipseq
clusterStab
codelink
codetoolsBioC
convert
copa
cosmo
cosmoGUI
crlmm
ctc
daMA
diffGeneAnalysis
domainsignatures
dualKS
dyebias
ecolitk
edd
edgeR
exonmap
explorase
externalVector
factDesign
fbat
fdrame
flagme
flowClust
flowCore
flowDB
flowFP
flowFlowJo
flowMerge
flowQ
flowStats
flowUtils
flowViz
gaga
gaggle
gcrma
genArise
gene2pathway
geneRecommender
genefilter
geneplotter
genomeIntervals
globaltest
goCluster
goProfiles
goTools
gpls
graph
hexbin
hopach
hypergraph
iFlow
idiogram
impute
iterativeBMA
iterativeBMAsurv
keggorth
lapmix
limma
limmaGUI
logicFS
logitT
lumi
maCorrPlot
maDB
maSigPro
maanova
macat
made4
maigesPack
makePlatformDesign
makecdfenv
marray
matchprobes
mdqc
metaArray
metahdep
methylumi
miRNApath
microRNA
minet
multiscan
multtest
ncdfExts
nem
nnNorm
nudge
occugene
oligo
oligoClasses
oneChannelGUI
ontoTools
pairseqsim
pamr
panp
parody
pathRender
pcaMethods
pcot2
pdInfoBuilder
pdmclass
pgUtils
pickgene
pkgDepTools
plateCore
plgem
plier
plw
ppiStats
prada
preprocessCore
prism
puma
qpcrNorm
qpgraph
quantsmooth
qvalue
rHVDM
rMAT
rama
rbsurv
reb
rfcprim
rflowcyt
rhdf5
rnaSeqTests
rsbml
rtracklayer
safe
sagenhaft
seqLogo
sigPathway
siggenes
simpleaffy
simulatorAPMS
sizepower
smoothMiner
snapCGH
snpMatrix
spikeLI
spkTools
splicegear
splots
spotSegmentation
sscore
ssize
stam
stepNorm
syslibGTK
tilingArray
timecourse
tkWidgets
topGO
tspair
twilight
vbmp
vsn
weaver
webbioc
widgetInvoke
widgetTools
xcms
xcmsGUI
xmapbridge
xps
yaqcaffy


Subscribe
Subscribe to the Bioconductor Changlog.


       
Thu, 02 Jul 2009

Biostrings
Use closest integer mismatch in trimLRPatterns when mismatch parameter is in (0,1).

[/Biostrings] permanent link

GGtools
pass chk
minor import change

[/GGtools] permanent link

RmiR
Change to use RmiR.Hs.miRNA

[/RmiR] permanent link

CAMERA
Fix getpspectra(), now using same colnames as originat xcmsSet, instead of hardcoded ones

[/CAMERA] permanent link

ShortRead
the 'coverage' instead of the 'pileup' function and hence works
with 'Rle' vectors throughout.

[/ShortRead] permanent link

HilbertVis
changed shrinkVector and plotLongVector to support Rle vectors
Fixed to minor typos.
updated vignette to mention that hilbertDisplay now supports Rle vectors

[/HilbertVis] permanent link

arrayQualityMetrics
Correct the matching of slots between R code and man pages

[/arrayQualityMetrics] permanent link

BSgenome
gdreduce, 'Reduce' sereral GenomeData or one GenomeDataList to GenomeData

[/BSgenome] permanent link

IRanges
Minor code changes to coverage calculation to provide minor speed ups.
Sped up coverage execution for IRanges objects.
Fixed man page to agree with code.
Removed extra } from man page.
Added missing closing } in man page.
Update chain file reading for new List infrastructure.
RangedData now automatically coerces its first argument to a
RangedData, if it's not a Ranges. Add coercion from
data.frame/DataTable to RangedData.

[/IRanges] permanent link

rtracklayer
The error handler in the HTML parser now allows for an empty 'level' argument.
Support coercion of first argument in GenomicData. Rename 'chrom' to
'space' for data frame objects.
Tweak demo and vignette.
Ensure scores are numeric in BED output.

[/rtracklayer] permanent link

plateCore
Working on man pages and commenting code.
Working on man pages and commenting code.
Working on man pages and commenting code.
Removed all data driven normFilter gates from examples to decrease R CMD check runtime.
Reduced size of sample data set, ran vignette again.
Reduced size of sample data set.
Cleaning up errors from R check
Cleaning up errors from R check
Fixed problem matching sampleNames in plotPlate
Fixed problem matching sampleNames in plotPlate
Fixed a bug in fpbind that was causing problems merging identical plates.
Fixed a bug in fpbind that was causing problems merging identical plates.
Cleaning up errors from R check
Cleaning up errors from R check
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Fixing R CMD Check problems.
Trying to get package in shape for release. Updating man pages
Trying to get package in shape for release. Updating man pages
Trying to get package in shape for release. Updating man pages
Updating plateCore vignette

[/plateCore] permanent link

affycoretools
Added imports(AnnotationDbi, get) so things like get(goid, GOTERM) will work.

[/affycoretools] permanent link

CNTools
A bug fix on the mapping of segment value to genes

[/CNTools] permanent link

crlmm
update computeCopynumber, added .R files for new classes/methods

[/crlmm] permanent link

Rgraphviz
Fixed a configure bug, updated README

[/Rgraphviz] permanent link

flowStats
fixed some bugs in peakSeperator.R and landmarkMatrix.R.
fixed a bug in landmarkMatrix.R.
bumped up version number to 1.3.8
Fixed function pruneRegions -- if the areas of the polygons are too
small, then do not collapses them.
edited gpaSet's man page
edit gpaSet's man page
Added an example in gpaSet.R using normalization object and work flow.

[/flowStats] permanent link

HilbertVisGUI
- hilbertDisplay and hilbertDisplayThreeColor now accept
Rle vectors (from IRanges)
- hilbertDisplayThreeColor now deals more sensibly with
data of different length
- the GUI understands the mnemonic keys Alt-P and Alt-N to
cycle through the data vectors

[/HilbertVisGUI] permanent link

cghMCR
Minor change to the plot function
Smaller sample data replaced the large ones.
One more large file removed
Large data files removed

[/cghMCR] permanent link

beadarraySNP
Handle missing data in report files in function read.SnpSetIllumina()

[/beadarraySNP] permanent link

iFlow
adding normal menu
again
playing
fix bugs
fix bugs

[/iFlow] permanent link

ArrayExpress
Replace sampleNames(dat) by sampleNames(dat) for NChannelSet

[/ArrayExpress] permanent link

flowUtils
storing tag defaults in an xml file now
changing extension to capital R and adding dependcies
Adding functionality to write FlowJo workspaces from workflow objects
Deleting Emacs temp file that were checked in

[/flowUtils] permanent link

biocViews
Save data in sqlite2 format.
Added DNACopyNumber to the biocViews ontology.

[/biocViews] permanent link

flowCore
Fixed issue with the wrong min range when reading in a fcs file , bumped version no
making sure the range parameter is ignored for clipping after the data has been transformed

[/flowCore] permanent link

AnnotationDbi
Overloads the Term and related methods for GOTERM
This update overloads the Term, Ontology etc. methods for GOTERM so
that they can take IDs or GOTermsAnnDbBimap.

[/AnnotationDbi] permanent link

Sun, 28 Jun 2009

affycoretools
Small fix to hyperGoutput. The output of annotation(GOHyperGResult) no longer contains the .db suffix, so this has to be added back on.

[/affycoretools] permanent link

Sat, 27 Jun 2009

EBImage
fixed noGTK support
minor
fix noGTK support in display.c

[/EBImage] permanent link

cghMCR
Vignette modified and SGOL algorithm and sample data added.

[/cghMCR] permanent link

plateCore
Updating plateCore vignette
Cleaning up plateCore files, getting ready for release.

[/plateCore] permanent link

affyPara
error in justvsnPara removed

[/affyPara] permanent link

Biostrings
Bumped version to 2.13.22 in order to release the new code for fast matching of the head/tail of a PDict object. In some situations where the head/tail is very narrow (<= 8b in total), the overall speed up for matchPDict() can be 10x or more.

[/Biostrings] permanent link

flowFP
Edited the man page for flowFPModel to indicate that a flowSet is collapsed to a flowFrame for binning.
Minor changes to the vignette to show the use of named parameters in addition to numbered parameters.
Previous change bumped version.
Fixed bug in flowPlex construction. Checks the number of instances as well as
the sample names of each instance for consistency.
Added excludeTime (default TRUE) to the model constructor so that if the user
want to consider all of the parameters in an fcs file, the constructor will
attempt to exclude the parameter containing time, if it is found.
Added 'bin_cols' to model plotting, allowing the user to supply colors to the
plotted bins, for model plotting.
Removed '<' symbol from the 'qc' and 'fancy plot color legend.
Removed references in the make system, (configure.ac) to BLAS and the gsl
library.
Removed aclocal.m4 file which is no longer needed.

[/flowFP] permanent link

KEGGgraph
version bump to 1.1.9: KEGGgraph software supports multiple substrates/products in KGML reaction from version 1.1.9.

[/KEGGgraph] permanent link

bioDist
improved implementation of KLdist functions

[/bioDist] permanent link

ROC
minor changes to doc and enhanced selection of C interface for dxrule.sca

[/ROC] permanent link

crlmm
added classes/methods for intermediate files and copy number analysis; added wrapper for preprocessing and genotypes.

[/crlmm] permanent link

globaltest
- fixed a bug in inheritance() sometimes causing a unended processing of the function.
- removed redundant levels in factor response in gt()
- transpose option fixed
- fixed the possibility of providing weights as a list of named vectors

[/globaltest] permanent link

EBImage
new installation in inst/doc

[/EBImage] permanent link

Fri, 26 Jun 2009

plateCore
updated the isogates function so that you can ignore the low values if you want.
there is now an argument minCut=NULL. when it is NULL, then nothing is done and so existing results won't be changed. If you supply an argument, typically 10, then these values will be omitted when calculating the percentiles.
comments on paper and reviewers

[/plateCore] permanent link

XDE
added seed to XdeParameter-class man page

[/XDE] permanent link