search

waldronlab / cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
https://waldronlab.io/cBioPortalData/
30 stars 12 forks source link

cbio <- cBioPortal() does not work #35

Closed ryao-mdanderson closed 3 years ago

ryao-mdanderson commented 3 years ago

Greetings,

I installed cBioPortalData on R/4.0.0 on our institution HPC cluster. however I failed to use cBioPortal(), $ module load R/4.0.0 $ R $library(cBioPortalData)

cbio <- cBioPortal() Error in Service(service = "cBioPortal", host = hostname, config = httr::config(ssl_verifypeer = 0L, : unused arguments (api_reference_url = apiUrl, api_reference_md5sum = "b39b387c6fdd8b04badf38cb0777998f")

May you please advise what's the reason and how to fix?

Thanks, Rong Yao

LiNk-NY commented 3 years ago

Hi Rong Yao, @ryao-mdanderson Please make sure you have a valid Bioconductor installation by checking BiocManager::valid(). With R >= 4.0.0, you should have either Bioc 3.12 or 3.13 installed. Can you provide more information on what sessionInfo() returns?

ryao-mdanderson commented 3 years ago

Hello,

Thanks for your quick response.

Our R 4.0.0 has Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)

Here is what the sessionInfo() returns

sessionInfo()

R version 4.0.0 (2020-04-24)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Red Hat Enterprise Linux

Matrix products: default

BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

[7] LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] parallel stats4 stats graphics grDevices utils datasets

[8] methods base

other attached packages:

[1] cBioPortalData_2.3.3 MultiAssayExperiment_1.14.0

[3] SummarizedExperiment_1.18.1 DelayedArray_0.14.0

[5] matrixStats_0.56.0 Biobase_2.48.0

[7] GenomicRanges_1.40.0 GenomeInfoDb_1.24.0

[9] IRanges_2.22.2 S4Vectors_0.26.1

[11] BiocGenerics_0.34.0 AnVIL_1.0.3

[13] dplyr_1.0.0

loaded via a namespace (and not attached):

[1] httr_1.4.1 bit64_0.9-7

[3] jsonlite_1.6.1 splines_4.0.0

[5] assertthat_0.2.1 askpass_1.1

[7] TCGAutils_1.10.0 BiocFileCache_1.12.0

[9] blob_1.2.1 Rsamtools_2.4.0

[11] GenomeInfoDbData_1.2.3 RTCGAToolbox_2.20.0

[13] yaml_2.2.1 progress_1.2.2

[15] pillar_1.4.4 RSQLite_2.2.0

[17] lattice_0.20-41 glue_1.4.1

[19] limma_3.44.1 digest_0.6.25

[21] XVector_0.28.0 rvest_0.3.6

[23] Matrix_1.2-18 XML_3.99-0.3

[25] pkgconfig_2.0.3 biomaRt_2.44.1

[27] zlibbioc_1.34.0 purrr_0.3.4

[29] RCircos_1.2.1 rapiclient_0.1.3

[31] BiocParallel_1.22.0 tibble_3.0.1

[33] openssl_1.4.1 generics_0.0.2

[35] ellipsis_0.3.1 GenomicFeatures_1.40.1

[37] survival_3.1-12 RJSONIO_1.3-1.4

[39] magrittr_1.5 crayon_1.3.4

[41] memoise_1.1.0 xml2_1.3.2

[43] tools_4.0.0 data.table_1.12.8

[45] prettyunits_1.1.1 hms_0.5.3

[47] formatR_1.7 lifecycle_0.2.0

[49] stringr_1.4.0 AnnotationDbi_1.50.0

[51] lambda.r_1.2.4 Biostrings_2.56.0

[53] compiler_4.0.0 rlang_0.4.6

[55] futile.logger_1.4.3 grid_4.0.0

[57] GenomicDataCommons_1.12.0 RCurl_1.98-1.2

[59] rappdirs_0.3.1 bitops_1.0-6

[61] DBI_1.1.0 curl_4.3

[63] R6_2.4.1 GenomicAlignments_1.24.0

[65] rtracklayer_1.48.0 bit_4.0.4

[67] futile.options_1.0.1 readr_1.3.1

[69] stringi_1.4.6 RaggedExperiment_1.12.0

[71] Rcpp_1.0.4.6 vctrs_0.3.0

[73] dbplyr_1.4.4 tidyselect_1.1.0

Thanks, Rong

From: Marcel Ramos notifications@github.com Reply-To: waldronlab/cBioPortalData reply@reply.github.com Date: Wednesday, November 25, 2020 at 10:58 AM To: waldronlab/cBioPortalData cBioPortalData@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Mention mention@noreply.github.com Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

Hi Rong Yao, @ryao-mdandersonhttps://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!1hV6O8fEs4MmehGNux-jgu1kG4qScwfcPGkx3MEVIs87AsAc_G6klWP08XF-2HA$ Please make sure you have a valid Bioconductor installation by checking BiocManager::valid(). With R >= 4.0.0, you should have either Bioc 3.12 or 3.13 installed. Can you provide more information on what sessionInfo() returns?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/issues/35*issuecomment-733829193__;Iw!!PfbeBCCAmug!1hV6O8fEs4MmehGNux-jgu1kG4qScwfcPGkx3MEVIs87AsAc_G6klWP0T0DgHIE$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AOGQX3EKPCGJI52Y6S2U5S3SRUZR5ANCNFSM4UCUVPFA__;!!PfbeBCCAmug!1hV6O8fEs4MmehGNux-jgu1kG4qScwfcPGkx3MEVIs87AsAc_G6klWP01Bh1cG4$.

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

LiNk-NY commented 3 years ago

Hi Rong Yao, @ryao-mdanderson

You're using the a 'too-new' version of cBioPortalData for the Bioconductor version that you have installed.

I would strongly recommend that you update your version of Bioconductor to 3.12 by using BiocManager::install(version = '3.12') but make sure that you have an appropriate location for the new package installations... See the BiocManager vignette for managing multiple Bioconductor versions.

Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You can re-install it using BiocManager::install("cBioPortalData").

Best, Marcel

ryao-mdanderson commented 3 years ago

Thank you, Marcel. I will try.

Happy Thanksgiving! Rong

From: Marcel Ramos notifications@github.com Reply-To: waldronlab/cBioPortalData reply@reply.github.com Date: Wednesday, November 25, 2020 at 4:07 PM To: waldronlab/cBioPortalData cBioPortalData@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Mention mention@noreply.github.com Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

Hi Rong Yao, @ryao-mdandersonhttps://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SL0mmSE$

You're using the a 'too-new' version of cBioPortalData for the Bioconductor version that you have installed.

I would strongly recommend that you update your version of Bioconductor to 3.12 by using BiocManager::install(version = '3.12') but make sure that you have an appropriate location for the new package installations... See the BiocManager vignettehttps://urldefense.com/v3/__https:/cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SkHRSdU$ for managing multiple Bioconductor versions.

Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You can re-install it using BiocManager::install("cBioPortalData").

Best, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/issues/35*issuecomment-733966856__;Iw!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4sMyeacM$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AOGQX3CDXYWGTBTNK423KZDSRV5XJANCNFSM4UCUVPFA__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4X6I4koo$.

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

LiNk-NY commented 3 years ago

Feel free to re-open if you are having issues. AFAIK they should be resolved. Best, Marcel

ryao-mdanderson commented 3 years ago

Hello Marcel,

Thank you for your suggestion. Today, I followed your alternative suggestion: “Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You can re-install it using BiocManager::install("cBioPortalData").

I reinstall cBioPortalData, the installation is successful. I am able to test : $ module load R/4.0.0 $ R

packageVersion("cBioPortalData") [1] ‘2.0.10’ cbio <- cBioPortal()

this success!

laml <- cBioDataPack("laml_tcga")

Output as the following:

Study file in cache: laml_tcga

Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_cna_hg19.seg

Parsed with column specification:

cols(

ID = col_character(),

chrom = col_double(),

loc.start = col_double(),

loc.end = col_double(),

num.mark = col_double(),

seg.mean = col_double()

)

Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_CNA.txt

Parsed with column specification:

cols(

.default = col_double(),

Hugo_Symbol = col_character()

)

See spec(...) for full column specifications.

|=================================================================| 100% 9 MB

Parsed with column specification:

cols(

Hugo_Symbol = col_character()

)

Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_linear_CNA.txt

Parsed with column specification:

cols(

.default = col_double(),

Hugo_Symbol = col_character()

)

See spec(...) for full column specifications.

|=================================================================| 100% 29 MB

Parsed with column specification:

cols(

Hugo_Symbol = col_character()

)

Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_methylation_hm27.txt

Parsed with column specification:

cols(

.default = col_double(),

Hugo_Symbol = col_character()

)

See spec(...) for full column specifications.

Parsed with column specification:

cols(

Hugo_Symbol = col_character()

)

Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_methylation_hm450.txt

Parsed with column specification:

cols(

.default = col_double(),

Hugo_Symbol = col_character()

)

See spec(...) for full column specifications.

Parsed with column specification:

cols(

Hugo_Symbol = col_character()

)

Working on: /tmp/RtmpCBSQek/136c70be6467_laml_tcga/data_mutations_extended.txt

Parsed with column specification:

cols(

.default = col_character(),

Entrez_Gene_Id = col_double(),

Start_Position = col_double(),

End_Position = col_double(),

dbSNP_Val_Status = col_logical(),

Score = col_double(),

t_ref_count = col_double(),

t_alt_count = col_double(),

n_ref_count = col_double(),

n_alt_count = col_double(),

Protein_position = col_double(),

Hotspot = col_double(),

RNAVAF_WU = col_double(),

RNAVarReads_WU = col_double(),

stop = col_double(),

NormalVAF_WU = col_double(),

start = col_double(),

TumorVAF_WU = col_double(),

RNARefReads_WU = col_double()

)

See spec(...) for full column specifications.

Parsed with column specification:

cols(

.default = col_character()

)

See spec(...) for full column specifications.

Error in .local(x, ...) : strand values must be in '+' '-' '*'

In addition: Warning messages:

1: In .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :

cannnot determine seqnames column unambiguously

2: In .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :

cannnot determine seqnames column unambiguously

3: In .find_seqnames_col(df_colnames0, seqnames.field0, xfix) :

cannnot determine seqnames column unambiguously

May you please advise what could be the cause of the error? How to fix?

Thank you very much for your help! Rong

From: "Yao,Rong" RYao@mdanderson.org Date: Wednesday, November 25, 2020 at 9:54 PM To: waldronlab/cBioPortalData reply@reply.github.com, waldronlab/cBioPortalData cBioPortalData@noreply.github.com Cc: Mention mention@noreply.github.com Subject: Re: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)

Thank you, Marcel. I will try.

Happy Thanksgiving! Rong

From: Marcel Ramos notifications@github.com Reply-To: waldronlab/cBioPortalData reply@reply.github.com Date: Wednesday, November 25, 2020 at 4:07 PM To: waldronlab/cBioPortalData cBioPortalData@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Mention mention@noreply.github.com Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

Hi Rong Yao, @ryao-mdandersonhttps://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SL0mmSE$

You're using the a 'too-new' version of cBioPortalData for the Bioconductor version that you have installed.

I would strongly recommend that you update your version of Bioconductor to 3.12 by using BiocManager::install(version = '3.12') but make sure that you have an appropriate location for the new package installations... See the BiocManager vignettehttps://urldefense.com/v3/__https:/cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4SkHRSdU$ for managing multiple Bioconductor versions.

Alternatively, the appropriate version of cBioPortalData for Bioconductor 3.11 is cBioPortalData_2.0.10. You can re-install it using BiocManager::install("cBioPortalData").

Best, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/issues/35*issuecomment-733966856__;Iw!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4sMyeacM$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AOGQX3CDXYWGTBTNK423KZDSRV5XJANCNFSM4UCUVPFA__;!!PfbeBCCAmug!zWAqL4ybW0Aq_jrDPlNFhRevvFkAoQaPj4cYKvZin3pbW8Um8MRM-WR4X6I4koo$.

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

LiNk-NY commented 3 years ago

Hi Rong Yao, @ryao-mdanderson

From the error, it looks like there is an issue with the dataset. Perhaps you may want to report it here: https://github.com/cBioPortal/datahub.

All datasets are not guaranteed to build as MultiAssayExperiment data objects with older versions of cBioPortalData. We recommend using the latest version of R and cBioPortalData.

It is more likely that they build now since our success rate is around 83% for packaged studies. We have also added functionality to only download the data in the case where the MultiAssayExperiment build is not working. These are some of the features in the newest version of the package.

Best regards, Marcel

ryao-mdanderson commented 3 years ago

Hello Marcel,

Thank you for your suggestion.

Just be curious, for cBioPortalData 2.0.10, laml <- cBioDataPack("laml_tcga") Access the website: https://cbioportal-datahub.s3.amazonaws.com to download data.

I also find dataset in https://github.com/cBioPortal/datahubhttps://urldefense.com/v3/__https:/github.com/cBioPortal/datahub__;!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1XlrlysPPXTI$ e.g. https://github.com/cBioPortal/datahub/tree/master/public/laml_tcga

In the new version of cBioPortalData, which is the above website that cBioDataPack() actually will access to download data? I am asking this, our HPC cluster has firewall restriction, it is better to know which url or both url(s) to for firewall open.

Thank you! Rong

From: Marcel Ramos notifications@github.com Reply-To: waldronlab/cBioPortalData reply@reply.github.com Date: Wednesday, December 2, 2020 at 3:44 PM To: waldronlab/cBioPortalData cBioPortalData@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Mention mention@noreply.github.com Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

Hi Rong Yao, @ryao-mdandersonhttps://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1XlrlLrv98u0$

From the error, it looks like there is an issue with the dataset. Perhaps you may want to report it here: https://github.com/cBioPortal/datahubhttps://urldefense.com/v3/__https:/github.com/cBioPortal/datahub__;!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1XlrlysPPXTI$.

All datasets are not guaranteed to build as MultiAssayExperiment data objects with older versions of cBioPortalData. We recommend using the latest version of R and cBioPortalData.

It is more likely that they build now since our success rate is around 83% for packaged studies. We have also added functionality to only download the data in the case where the MultiAssayExperiment build is not working. These are some of the features in the newest version of the package.

Best regards, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/issues/35*issuecomment-737514218__;Iw!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1Xlrl2-KNtaM$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AOGQX3EJX5LJPJNGDHYEDBDSS2YIRANCNFSM4UCUVPFA__;!!PfbeBCCAmug!xbfMBQowNussIe5xTkKZq8hfZbC0xL418xjqEH-IzUExf9zEqLT1XlrlcUdTQTA$.

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

LiNk-NY commented 3 years ago

Hi Rong, @ryao-mdanderson

cBioPortalData version 2.0.10 (and newer) uses the AWS URL https://cbioportal-datahub.s3.amazonaws.com. You can see the code here: https://github.com/waldronlab/cBioPortalData/blob/RELEASE_3_11/R/cBioDataPack.R#L2

Best, Marcel

ryao-mdanderson commented 3 years ago

Hi Marcel,

Thank you for your information.

Have a good night. Rong

From: Marcel Ramos notifications@github.com Reply-To: waldronlab/cBioPortalData reply@reply.github.com Date: Wednesday, December 2, 2020 at 6:47 PM To: waldronlab/cBioPortalData cBioPortalData@noreply.github.com Cc: "Yao,Rong" RYao@mdanderson.org, Mention mention@noreply.github.com Subject: [EXT] Re: [waldronlab/cBioPortalData] cbio <- cBioPortal() does not work (#35)

WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.

Hi Rong, @ryao-mdandersonhttps://urldefense.com/v3/__https:/github.com/ryao-mdanderson__;!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroRsnLCJhs$

cBioPortalData version 2.0.10 (and newer) uses the AWS URL https://cbioportal-datahub.s3.amazonaws.comhttps://urldefense.com/v3/__https:/cbioportal-datahub.s3.amazonaws.com__;!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroRBU5raC4$. You can see the code here: https://github.com/waldronlab/cBioPortalData/blob/RELEASE_3_11/R/cBioDataPack.R#L2https://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/blob/RELEASE_3_11/R/cBioDataPack.R*L2__;Iw!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroRyuVyIwM$

Best, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/waldronlab/cBioPortalData/issues/35*issuecomment-737585920__;Iw!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroRRqjrvpM$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AOGQX3HQRHCLJNV7AUPIMPLSS3NYBANCNFSM4UCUVPFA__;!!PfbeBCCAmug!0sWqaxPF5fxYFWBUW2mCHxfmL3YkpsZZGbEB0bEMME9yPZtXGW9UkroR603z-bU$.

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.