Re: [Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
Hi Shraddha,
I am also unable to reproduce this in RStudio Server Version 1.4.1106 using
our Bioc 3.12 Docker container.
There may be some inadvertent version mixing based on the error.
Please make sure the `BiocManager::valid()` is returning `TRUE`.
---
> brca <- curatedTCGAData::curatedTCGAData("BRCA", c("miRNASeqGene",
"mRNAArray", "RPPAArray", "Methylation_methyl27"), dry.run=FALSE)
> brca
A MultiAssayExperiment object of 4 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 4:
[1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows
and 849 columns
[2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and
590 columns
[3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and
937 columns
[4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with
27578 rows and 343 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save all data to files
> assays(experiments(brca)[[4]])
List of length 1
names(1): counts
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS
Matrix products: default
BLAS/LAPACK:
/usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
methods base
other attached packages:
[1] rhdf5_2.34.0 curatedTCGAData_1.12.1
MultiAssayExperiment_1.16.0
[4] SummarizedExperiment_1.20.0 Biobase_2.50.0 GenomicRanges_1.42.0
[7] GenomeInfoDb_1.26.7 IRanges_2.24.1 S4Vectors_0.28.1
[10] BiocGenerics_0.36.1 MatrixGenerics_1.2.1 matrixStats_0.59.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lattice_0.20-41 assertthat_0.2.1
[4] digest_0.6.27 utf8_1.2.1 mime_0.10
[7] BiocFileCache_1.14.0 R6_2.5.0 RSQLite_2.2.7
[10] httr_1.4.2 pillar_1.6.1 zlibbioc_1.36.0
[13] rlang_0.4.11 curl_4.3.1 blob_1.2.1
[16] Matrix_1.3-2 AnnotationHub_2.22.1 RCurl_1.98-1.3
[19] bit_4.0.4 HDF5Array_1.18.1 shiny_1.6.0
[22] DelayedArray_0.16.3 compiler_4.0.3 httpuv_1.6.1
[25] pkgconfig_2.0.3 htmltools_0.5.1.1 tidyselect_1.1.1
[28] tibble_3.1.2 GenomeInfoDbData_1.2.4
interactiveDisplayBase_1.28.0
[31] fansi_0.5.0 withr_2.4.2 crayon_1.4.1
[34] dplyr_1.0.6 dbplyr_2.1.1 later_1.2.0
[37] rhdf5filters_1.2.1 bitops_1.0-7 rappdirs_0.3.3
[40] grid_4.0.3 xtable_1.8-4 lifecycle_1.0.0
[43] DBI_1.1.1 magrittr_2.0.1 cachem_1.0.5
[46] XVector_0.30.0 promises_1.2.0.1 ellipsis_0.3.2
[49] generics_0.1.0 vctrs_0.3.8 Rhdf5lib_1.12.1
[52] tools_4.0.3 bit64_4.0.5 glue_1.4.2
[55] purrr_0.3.4 BiocVersion_3.12.0 fastmap_1.1.0
[58] yaml_2.2.1 AnnotationDbi_1.52.0
ExperimentHub_1.16.1
[61] BiocManager_1.30.15 memoise_2.0.0
---
Best,
Marcel
On 6/3/21 11:21 AM, Vincent Carey wrote:
> On Thu, Jun 3, 2021 at 9:11 AM Shraddha Pai
> wrote:
>
>> Hi Vincent,
>> Thank you. This is for a workshop with pre-selected versions of R/BioC, so
>> I have no control over the release.
>> Will try redownloading the data. I just found it puzzling that the
>> identical code works in command-line R (ie started from bash shell) but not
>> in Rstudio but perhaps they have different ways of caching loaded MAE
>> objects?
>> Best,Shraddha
>>
> I neglected to mention that my transcript was developed in RStudio on
> Terra, with RStudio 1.4.1106, 2389bc24
>
>
>> On Wed, Jun 2, 2021 at 4:28 PM Vincent Carey
>> wrote:
>>
>>> You are behind the release and should update. However, with a reasonably
>>> close
>>> instance I can't reproduce your error. I had a flaky download at one
>>> point; you might
>>> want to reconstitute your brca data.
>>>
brca = curatedTCGAData("BRCA", c("miRNASeqGene", "mRNAArray", "RPPAArray",
"Methylation_methyl27"), dry.run=FALSE)snapshotDate(): 2020-10-27Working
on: BRCA_miRNASeqGene-20160128see ?curatedTCGAData and
browseVignettes('curatedTCGAData') for documentationdownloading 1
resourcesretrieving 1 resource
|==
Re: [Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
On Thu, Jun 3, 2021 at 9:11 AM Shraddha Pai
wrote:
> Hi Vincent,
> Thank you. This is for a workshop with pre-selected versions of R/BioC, so
> I have no control over the release.
> Will try redownloading the data. I just found it puzzling that the
> identical code works in command-line R (ie started from bash shell) but not
> in Rstudio but perhaps they have different ways of caching loaded MAE
> objects?
> Best,Shraddha
>
I neglected to mention that my transcript was developed in RStudio on
Terra, with RStudio 1.4.1106, 2389bc24
>
> On Wed, Jun 2, 2021 at 4:28 PM Vincent Carey
> wrote:
>
>> You are behind the release and should update. However, with a reasonably
>> close
>> instance I can't reproduce your error. I had a flaky download at one
>> point; you might
>> want to reconstitute your brca data.
>>
>> > brca = curatedTCGAData("BRCA", c("miRNASeqGene", "mRNAArray", "RPPAArray",
>> > "Methylation_methyl27"), dry.run=FALSE)snapshotDate(): 2020-10-27Working
>> > on: BRCA_miRNASeqGene-20160128see ?curatedTCGAData and
>> > browseVignettes('curatedTCGAData') for documentationdownloading 1
>> > resourcesretrieving 1 resource
>> > |===|
>> > 100%loading from cacheWorking on: BRCA_mRNAArray-20160128see
>> > ?curatedTCGAData and browseVignettes('curatedTCGAData') for
>> > documentationdownloading 1 resourcesretrieving 1 resource
>> > |===|
>> > 100%loading from cacheWorking on: BRCA_RPPAArray-20160128see
>> > ?curatedTCGAData and browseVignettes('curatedTCGAData') for
>> > documentationdownloading 1 resourcesretrieving 1 resource
>> > |===|
>> > 100%loading from cacheWorking on: BRCA_Methylation_methyl27-20160128see
>> > ?curatedTCGAData and browseVignettes('curatedTCGAData') for
>> > documentationloading from cachesee ?curatedTCGAData and
>> > browseVignettes('curatedTCGAData') for documentationloading from
>> > cacheWorking on: BRCA_colData-20160128see ?curatedTCGAData and
>> > browseVignettes('curatedTCGAData') for documentationloading from
>> > cacheWorking on: BRCA_metadata-20160128see ?curatedTCGAData and
>> > browseVignettes('curatedTCGAData') for documentationloading from
>> > cacheWorking on: BRCA_sampleMap-20160128see ?curatedTCGAData and
>> > browseVignettes('curatedTCGAData') for documentationloading from
>> > cacheharmonizing input:
>> removing 11654 sampleMap rows not in names(experiments)
>> removing 1 colData rownames not in sampleMap 'primary'> brcaA
>> MultiAssayExperiment object of 4 listed
>> experiments with user-defined names and respective classes.
>> Containing an ExperimentList class object of length 4:
>> [1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849
>> columns
>> [2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590
>> columns
>> [3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937
>> columns
>> [4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578
>> rows and 343 columns
>> Functionality:
>> experiments() - obtain the ExperimentList instance
>> colData() - the primary/phenotype DataFrame
>> sampleMap() - the sample coordination DataFrame
>> `$`, `[`, `[[` - extract colData columns, subset, or experiment
>> *Format() - convert into a long or wide DataFrame
>> assays() - convert ExperimentList to a SimpleList of matrices
>> exportClass() - save all data to files> assay(experiments(brca)[[4]])<27578
>> x 343> matrix of class DelayedMatrix and type "double":
>>TCGA-A1-A0SD-01A-11D-A112-05 ... TCGA-E2-A15T-01A-11D-A112-05
>> cg0292 0.60555263 . 0.25951246
>> cg2426 0.06197412 . 0.04144839
>> cg3994 0.33345006 . 0.34969161
>> cg5847 0.67217034 . 0.83666264
>> cg6414 NA . NA
>>.... ..
>> cg27657283 0.04196141 . 0.03385843
>> cg27661264 0.51756951 . 0.47593756
>> cg27662379 0.01078112 . 0.01157093
>> cg27662877 0.03112835 . 0.02603354
>> cg27665659 0.01072116 . 0.01756740>
>> sessionInfo()R version 4.0.3 (2020-10-10)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 20.04 LTS
>>
>> Matrix products: default
>> BLAS/LAPACK:
>> /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> LC_TIME=en_US.UTF-8
>> [4] LC_COLLATE=en_
Re: [Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
Hi Vincent,
Thank you. This is for a workshop with pre-selected versions of R/BioC, so
I have no control over the release.
Will try redownloading the data. I just found it puzzling that the
identical code works in command-line R (ie started from bash shell) but not
in Rstudio but perhaps they have different ways of caching loaded MAE
objects?
Best,Shraddha
On Wed, Jun 2, 2021 at 4:28 PM Vincent Carey
wrote:
> You are behind the release and should update. However, with a reasonably
> close
> instance I can't reproduce your error. I had a flaky download at one
> point; you might
> want to reconstitute your brca data.
>
> > brca = curatedTCGAData("BRCA", c("miRNASeqGene", "mRNAArray", "RPPAArray",
> > "Methylation_methyl27"), dry.run=FALSE)snapshotDate(): 2020-10-27Working
> > on: BRCA_miRNASeqGene-20160128see ?curatedTCGAData and
> > browseVignettes('curatedTCGAData') for documentationdownloading 1
> > resourcesretrieving 1 resource
> > |===|
> > 100%loading from cacheWorking on: BRCA_mRNAArray-20160128see
> > ?curatedTCGAData and browseVignettes('curatedTCGAData') for
> > documentationdownloading 1 resourcesretrieving 1 resource
> > |===|
> > 100%loading from cacheWorking on: BRCA_RPPAArray-20160128see
> > ?curatedTCGAData and browseVignettes('curatedTCGAData') for
> > documentationdownloading 1 resourcesretrieving 1 resource
> > |===|
> > 100%loading from cacheWorking on: BRCA_Methylation_methyl27-20160128see ?cu
ratedTCGAData and browseVignettes('curatedTCGAData') for documentationloading
from cachesee ?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheWorking on: BRCA_colData-20160128see
?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheWorking on: BRCA_metadata-20160128see
?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheWorking on: BRCA_sampleMap-20160128see
?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheharmonizing input:
> removing 11654 sampleMap rows not in names(experiments)
> removing 1 colData rownames not in sampleMap 'primary'> brcaA
> MultiAssayExperiment object of 4 listed
> experiments with user-defined names and respective classes.
> Containing an ExperimentList class object of length 4:
> [1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849
> columns
> [2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590
> columns
> [3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937
> columns
> [4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows
> and 343 columns
> Functionality:
> experiments() - obtain the ExperimentList instance
> colData() - the primary/phenotype DataFrame
> sampleMap() - the sample coordination DataFrame
> `$`, `[`, `[[` - extract colData columns, subset, or experiment
> *Format() - convert into a long or wide DataFrame
> assays() - convert ExperimentList to a SimpleList of matrices
> exportClass() - save all data to files> assay(experiments(brca)[[4]])<27578
> x 343> matrix of class DelayedMatrix and type "double":
>TCGA-A1-A0SD-01A-11D-A112-05 ... TCGA-E2-A15T-01A-11D-A112-05
> cg0292 0.60555263 . 0.25951246
> cg2426 0.06197412 . 0.04144839
> cg3994 0.33345006 . 0.34969161
> cg5847 0.67217034 . 0.83666264
> cg6414 NA . NA
>.... ..
> cg27657283 0.04196141 . 0.03385843
> cg27661264 0.51756951 . 0.47593756
> cg27662379 0.01078112 . 0.01157093
> cg27662877 0.03112835 . 0.02603354
> cg27665659 0.01072116 . 0.01756740>
> sessionInfo()R version 4.0.3 (2020-10-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 20.04 LTS
>
> Matrix products: default
> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8LC_MESSAGES=C
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats4stats graphics grDevices utils datasets
Re: [Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
You are behind the release and should update. However, with a reasonably
close
instance I can't reproduce your error. I had a flaky download at one
point; you might
want to reconstitute your brca data.
> brca = curatedTCGAData("BRCA", c("miRNASeqGene", "mRNAArray", "RPPAArray",
> "Methylation_methyl27"), dry.run=FALSE)snapshotDate(): 2020-10-27Working on:
> BRCA_miRNASeqGene-20160128see ?curatedTCGAData and
> browseVignettes('curatedTCGAData') for documentationdownloading 1
> resourcesretrieving 1 resource
> |===|
> 100%loading from cacheWorking on: BRCA_mRNAArray-20160128see
> ?curatedTCGAData and browseVignettes('curatedTCGAData') for
> documentationdownloading 1 resourcesretrieving 1 resource
> |===|
> 100%loading from cacheWorking on: BRCA_RPPAArray-20160128see
> ?curatedTCGAData and browseVignettes('curatedTCGAData') for
> documentationdownloading 1 resourcesretrieving 1 resource
> |===|
> 100%loading from cacheWorking on: BRCA_Methylation_methyl27-20160128see ?cura
tedTCGAData and browseVignettes('curatedTCGAData') for documentationloading
from cachesee ?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheWorking on: BRCA_colData-20160128see
?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheWorking on: BRCA_metadata-20160128see
?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheWorking on: BRCA_sampleMap-20160128see
?curatedTCGAData and browseVignettes('curatedTCGAData') for
documentationloading from cacheharmonizing input:
removing 11654 sampleMap rows not in names(experiments)
removing 1 colData rownames not in sampleMap 'primary'> brcaA
MultiAssayExperiment object of 4 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 4:
[1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows
and 849 columns
[2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and
590 columns
[3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns
[4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with
27578 rows and 343 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save all data to files>
assay(experiments(brca)[[4]])<27578 x 343> matrix of class
DelayedMatrix and type "double":
TCGA-A1-A0SD-01A-11D-A112-05 ... TCGA-E2-A15T-01A-11D-A112-05
cg0292 0.60555263 . 0.25951246
cg2426 0.06197412 . 0.04144839
cg3994 0.33345006 . 0.34969161
cg5847 0.67217034 . 0.83666264
cg6414 NA . NA
.... ..
cg27657283 0.04196141 . 0.03385843
cg27661264 0.51756951 . 0.47593756
cg27662379 0.01078112 . 0.01157093
cg27662877 0.03112835 . 0.02603354
cg27665659 0.01072116 .
0.01756740> sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils
datasets methods base
other attached packages:
[1] rhdf5_2.34.0curatedTCGAData_1.12.1
MultiAssayExperiment_1.16.0
[4] SummarizedExperiment_1.20.0 Biobase_2.50.0
GenomicRanges_1.42.0
[7] GenomeInfoDb_1.26.7 IRanges_2.24.1
S4Vectors_0.28.1
[10] BiocGenerics_0.36.1 MatrixGenerics_1.2.1
matrixStats_0.59.0
[13] httr_1.4.2 magrittr_2.0.1
AnVIL_1.5.0
[16] dplyr_1.0.6 BiocManager_1.30.15
loaded via a namespace (and not attached):
[1] bitops_1.0-7 bit64_4.0.5
[3] rprojroot_2.0.2 tools_4.0.3
[5] R6_2.5.0
[Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio
Hello BioC community,
Calling assays() on a SummarizedExperiment object has suddenly started
giving me this error in Rstudio but not on command-line R. I have been
trying to solve this for a few hours without luck and any help would be
great. sessionInfo() output below and this is Rstudio 1.4.
Thanks,Shraddha
Browse[1]> brcaA MultiAssayExperiment object of 4 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 4:
[1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows
and 166 columns
[2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and
453 columns
[3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 362 columns
[4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with
27578 rows and 261 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save all data to files
Browse[1]> assays(experiments(brca)[[4]])Error in
.Call2("C_h5getdimscales", filepath, name, scalename, PACKAGE =
"HDF5Array") :
failed to open file '/root/.cache/ExperimentHub/661a6f10d826_2122'
Browse[2]> experiments(brca)[[4]]class: SummarizedExperiment
dim: 27578 261
metadata(0):
assays(1): counts
rownames(27578): cg0292 cg2426 ... cg27662877 cg27665659
rowData names(3): Gene_Symbol Chromosome Genomic_Coordinate
colnames(261): TCGA-A1-A0SD-01A-11D-A112-05 TCGA-A2-A04N-01A-11D-A112-05 ...
TCGA-E2-A15S-01A-11D-A112-05 TCGA-E2-A15T-01A-11D-A112-05
colData names(0):
> sessionInfo()R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils
datasets methods
[9] base
other attached packages:
[1] rhdf5_2.34.0netDx_1.2.3
[3] bigmemory_4.5.36curatedTCGAData_1.12.1
[5] MultiAssayExperiment_1.16.0 SummarizedExperiment_1.20.0
[7] Biobase_2.50.0 GenomicRanges_1.42.0
[9] GenomeInfoDb_1.26.7 IRanges_2.24.1
[11] S4Vectors_0.28.1BiocGenerics_0.36.1
[13] MatrixGenerics_1.2.1matrixStats_0.58.0
loaded via a namespace (and not attached):
[1] uuid_0.1-4AnnotationHub_2.22.1
[3] BiocFileCache_1.14.0 NMF_0.23.0
[5] plyr_1.8.6igraph_1.2.6
[7] RCy3_2.10.2 lazyeval_0.2.2
[9] splines_4.0.5 entropy_1.3.0
[11] BiocParallel_1.24.1 scater_1.18.6
[13] rncl_0.8.4ggplot2_3.3.3
[15] gridBase_0.4-7digest_0.6.27
[17] foreach_1.5.1 htmltools_0.5.1.1
[19] viridis_0.6.1 fansi_0.4.2
[21] magrittr_2.0.1memoise_2.0.0
[23] cluster_2.1.1 doParallel_1.0.16
[25] ROCR_1.0-11 limma_3.46.0
[27] annotate_1.68.0 R.utils_2.10.1
[29] prettyunits_1.1.1 colorspace_2.0-1
[31] blob_1.2.1rappdirs_0.3.3
[33] xfun_0.23 dplyr_1.0.6
[35] crayon_1.4.1 RCurl_1.98-1.3
[37] bigmemory.sri_0.1.3 graph_1.68.0
[39] genefilter_1.72.1 phylobase_0.8.10
[41] survival_3.2-10 iterators_1.0.13
[43] ape_5.5 glue_1.4.2
[45] registry_0.5-1gtable_0.3.0
[47] zlibbioc_1.36.0 XVector_0.30.0
[49] DelayedArray_0.16.3 BiocSingular_1.6.0
[51] kernlab_0.9-29Rhdf5lib_1.12.1
[53] shape_1.4.6 SingleCellExperiment_1.12.0
[55] HDF5Array_1.18.1 scales_1.1.1
[57] DBI_1.1.1 edgeR_3.32.1
[59] rngtools_1.5 Rcpp_1.0.6
[61] viridisLite_0.4.0 xtable_1.8-4
[63] progress_1.2.2rsvd_1.0.5
[65] bit_4.0.4 glmnet_4.1-1
[67] netSmooth_1.10.0 httr_1.4.2
[69] RColorBrewer_1.1-2ellipsis_0.3.2
[71] scuttle_1.0.4 pkgconfig_2.0.3
[73] XML_3.99-0.6 R.methodsS3_1.8.1
[75] dbplyr_2.1.1 locfit_1.5-9.4
[77] utf8_1.2.1RJSONIO_1.3-1.4
[79] howmany_0.3-1 tidyselect_1.1.1
[81] rlang_0.4.11 softImpute_1.4-1
[83] reshape2_1.4.4later_1.2.0
[85] Ann
