Re: [Bioc-devel] Is package name "ADAPT" available?
Thanks Hervé!
-Mukai
On Tue, Apr 9, 2024 at 5:34 PM Hervé Pagès
wrote:
> Also BiocManager::available() will show you all the packages in the
> CRAN/Bioconductor ecosystem that contain the specified string:
>
> > library(BiocManager)
> > available("ADAPT")
> [1] "adapt4pv""adaptalint" "adaptDiag"
> [4] "AdaptGauss" "adaptiveGPCA""AdaptiveSparsity"
> [7] "adaptivetau" "adaptIVPT" "adaptMCMC"
> [10] "adaptMT" "adaptr" "ADAPTS"
> [13] "adaptsmoFMRI""adaptTest" "BrokenAdaptiveRidge"
> [16] "eufmdis.adapt" "fairadapt" "fruclimadapt"
> [19] "GLMMadaptive""iAdapt" "kernstadapt"
> [22] "pcadapt" "survRM2adapt"
>
> Best,
>
> H.
> On 4/9/24 07:38, Mukai Wang wrote:
>
> Thank you Olly!
>
> -Mukai
>
> On Tue, Apr 9, 2024 at 10:31 AM Oliver Crook
>
> wrote:
>
>
> Hi Mukai,
>
> If you run biocCheck on your package it will tell you if the name is
> already taken.
>
> Best wishes,
> Olly
>
> ---
> Dr. Oliver Crook (he/him)
> Florence Nightingale Bicentennial Fellow, Department of Statistics
> Todd-Bird Junior Research Fellow, New College
> University of Oxford
> --
> *From:* Bioc-devel
> on behalf of Mukai
> Wang
> *Sent:* Tuesday, April 9, 2024 3:12 PM
> *To:* bioc-devel@r-project.org
>
> *Subject:* [Bioc-devel] Is package name "ADAPT" available?
>
> Dear bioconductor community,
>
> I am writing to ask if the package name ADAPT is available for use. I don't
> see any package with this name on bioconductor but there is a package
> called "adapt" archived many years ago on CRAN, so I am not sure. Any
> suggestion is appreciated!
>
> Best,
> Mukai
>
> --
> Mukai Wang
> Biostatistics Department, School of Public Health, University of Michigan
>
> [[alternative HTML version deleted]]
>
> ___bioc-de...@r-project.org
> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core teamhpages.on.git...@gmail.com
>
>
--
Mukai Wang
Biostatistics Department, School of Public Health, University of Michigan
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Is package name "ADAPT" available?
Also BiocManager::available() will show you all the packages in the
CRAN/Bioconductor ecosystem that contain the specified string:
> library(BiocManager)
> available("ADAPT")
[1] "adapt4pv" "adaptalint" "adaptDiag"
[4] "AdaptGauss" "adaptiveGPCA" "AdaptiveSparsity"
[7] "adaptivetau" "adaptIVPT" "adaptMCMC"
[10] "adaptMT" "adaptr" "ADAPTS"
[13] "adaptsmoFMRI" "adaptTest" "BrokenAdaptiveRidge"
[16] "eufmdis.adapt" "fairadapt" "fruclimadapt"
[19] "GLMMadaptive" "iAdapt" "kernstadapt"
[22] "pcadapt" "survRM2adapt"
Best,
H.
On 4/9/24 07:38, Mukai Wang wrote:
> Thank you Olly!
>
> -Mukai
>
> On Tue, Apr 9, 2024 at 10:31 AM Oliver Crook
> wrote:
>
>> Hi Mukai,
>>
>> If you run biocCheck on your package it will tell you if the name is
>> already taken.
>>
>> Best wishes,
>> Olly
>>
>> ---
>> Dr. Oliver Crook (he/him)
>> Florence Nightingale Bicentennial Fellow, Department of Statistics
>> Todd-Bird Junior Research Fellow, New College
>> University of Oxford
>> --
>> *From:* Bioc-devel on behalf of Mukai
>> Wang
>> *Sent:* Tuesday, April 9, 2024 3:12 PM
>> *To:*bioc-devel@r-project.org
>> *Subject:* [Bioc-devel] Is package name "ADAPT" available?
>>
>> Dear bioconductor community,
>>
>> I am writing to ask if the package name ADAPT is available for use. I don't
>> see any package with this name on bioconductor but there is a package
>> called "adapt" archived many years ago on CRAN, so I am not sure. Any
>> suggestion is appreciated!
>>
>> Best,
>> Mukai
>>
>> --
>> Mukai Wang
>> Biostatistics Department, School of Public Health, University of Michigan
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Is package name "ADAPT" available?
Thank you Olly! -Mukai On Tue, Apr 9, 2024 at 10:31 AM Oliver Crook wrote: > Hi Mukai, > > If you run biocCheck on your package it will tell you if the name is > already taken. > > Best wishes, > Olly > > --- > Dr. Oliver Crook (he/him) > Florence Nightingale Bicentennial Fellow, Department of Statistics > Todd-Bird Junior Research Fellow, New College > University of Oxford > -- > *From:* Bioc-devel on behalf of Mukai > Wang > *Sent:* Tuesday, April 9, 2024 3:12 PM > *To:* bioc-devel@r-project.org > *Subject:* [Bioc-devel] Is package name "ADAPT" available? > > Dear bioconductor community, > > I am writing to ask if the package name ADAPT is available for use. I don't > see any package with this name on bioconductor but there is a package > called "adapt" archived many years ago on CRAN, so I am not sure. Any > suggestion is appreciated! > > Best, > Mukai > > -- > Mukai Wang > Biostatistics Department, School of Public Health, University of Michigan > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Mukai Wang Biostatistics Department, School of Public Health, University of Michigan [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Is package name "ADAPT" available?
Hi Mukai, If you run biocCheck on your package it will tell you if the name is already taken. Best wishes, Olly --- Dr. Oliver Crook (he/him) Florence Nightingale Bicentennial Fellow, Department of Statistics Todd-Bird Junior Research Fellow, New College University of Oxford From: Bioc-devel on behalf of Mukai Wang Sent: Tuesday, April 9, 2024 3:12 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Is package name "ADAPT" available? Dear bioconductor community, I am writing to ask if the package name ADAPT is available for use. I don't see any package with this name on bioconductor but there is a package called "adapt" archived many years ago on CRAN, so I am not sure. Any suggestion is appreciated! Best, Mukai -- Mukai Wang Biostatistics Department, School of Public Health, University of Michigan [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Is package name "ADAPT" available?
Dear bioconductor community, I am writing to ask if the package name ADAPT is available for use. I don't see any package with this name on bioconductor but there is a package called "adapt" archived many years ago on CRAN, so I am not sure. Any suggestion is appreciated! Best, Mukai -- Mukai Wang Biostatistics Department, School of Public Health, University of Michigan [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] List of Deprecated Packages for Bioc3.19
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. This is the current list of deprecated packages for Bioc 3.19. It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list Do not un-deprecate a package yourself. You must request un-deprecation from the Bioconductor core team at bioc-devel@r-project.org. Software: User Requested * CancerInSilico * cellHTS2 * CNVgears * compartmap * ensemblVEP * HumanTranscriptomeCompendium * maigesPack * MMAPPR2 * openPrimeRui * pwOmics * restfulSE Unresponsive: * beadarraySNP * BDMMAcorrect * BHC * biodbLipidmaps * BioNetStat * CancerSubtypes * cliqueMS * clusterSeq * contiBAIT * CoRegNet * CORREP * crisprseekplus * DNABarcodes * dpeak * eegc * enrichTF * exomePeak2 * farms * FCBF * flowMap * FoldGO * FScanR * FunChIP * GOSim * ImmuneSpaceR * InterMineR * IntOMICS * IRISFGM * iterClust * MetaVolcanoR * miRmine * MobilityTransformR * multiOmicsViz * MutationPatterns * NeighborNet * NetPathMiner * oneSENSE * pathVar * pcxn * PERFect * phemd * PloGO2 * proteasy * PSEA * RefPlus * ReQON * riboSeqR * RIPAT * RLSeq * segmentSeq * SeqSQC * SimBindProfiles * singleCellTK * SMAP * sparseDOSSA * SpidermiR * SQUADD * StarBioTrek * STROMA4 * TNBC.CMS * TnT ExperimentData: User Requested * MMAPPR2data * restfulSEData Unresponsive * pcxnData * RLHub Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Kern, Lori Sent: Thursday, February 29, 2024 2:40 PM To: bioc-devel@r-project.org Subject: List of Deprecated Packages for Bioc3.19 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. This is the current list of deprecated packages for Bioc 3.19. It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encourage anyone that is familiar with a package maintainer on this list to reach out to them and notify them directly. Packages can be un-deprecated if a maintainer fixes the package to build/check cleanly before the next release and requests un-deprecation on the bioc-devel@r-project.org mailing list Do not un-deprecate a package yourself. You must request un-deprecation from the Bioconductor core team at bioc-devel@r-project.org. Software: User Requested * CancerInSilico * cellHTS2 * CNVgears * compartmap * ensemblVEP * maigesPack * MMAPPR2 * openPrimeRui Unresponsive: * beadarraySNP * BDMMAcorrect * BHC * CancerSubtypes * clusterSeq * CNVPanelizer * contiBAIT * CoRegNet * CORREP * crisprseekplus * DNABarcodes * dpeak * eegc * enrichTF * exomePeak2 * farms * FCBF * flowMap * FoldGO * FScanR * gscreend * ImmuneSpaceR * InterMineR * IRISFGM * MetaVolcanoR * miRmine * MobilityTransformR * multiOmicsViz * MutationPatterns * NeighborNet * NetPathMiner * NeuCA * oneSENSE * pathVar * pcxn * PERFect * PloGO2 * proteasy * RefPlus * ReQON * riboSeqR * RIPAT * segmentSeq * SeqSQC * SimBindProfiles * singleCellTK * SMAP * sparseDOSSA * SpidermiR * SQUADD * StarBioTrek * STROMA4 * TNBC.CMS * TnT ExperimentData: User Requested * MMAPPR2data Unresponsive * pcxnData Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please
