Closed rezakj closed 5 years ago
Hi @rezakj
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: iCellR
Type: Package
Title: iCellR; A Feature-rich Interactive R Package to Work with
High-Throughput Single Cell Sequencing Technologies.
Version: 0.99.0
Authors: Alireza Khodadadi-Jamayran, Joseph Pucella, Hua Zhou, Nicole
Doudican, John Carucci, Adriana Heguy, Boris Reizis,
Aristotelis Tsirigos
Maintainer: The package maintainer;
Alireza Khodadadi-Jamayran,
Applied Bioinformatics Laboratories (ABL),
Genome Technology Center (GTC),
Division of Advanced Research Technologies (DART),
NYU Langone Medical Center,
550 1st Ave, SB-604/MSB-304, New York, NY 10016,
<alireza.khodadadi-jamayran@nyumc.org>
Description: Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq and CITE-seq). iCellR is an R package that allows scientists unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. iCellR allows users to design both unsupervised and supervised models to best suit their research. In addition, iCellR provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts and filling them with imputation methods, batch differences, pathway analysis and tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis.
Keywords: PCA, UMAP, Diffusion Map, tSNE, high throughput, single cell,
differential gene expression, analysis, clustering, PseudoTime,
dimension reduction, normalization, spike-in, scRNA-Seq,
CITE-Seq, scVDJ-Seq, data visualization, interactive plots, 3D
plots, cell type prediction, pathway analysis, batch
correction, cell cycle, cell gating, ADT, filtering,Clustering
methods: ward.D, ward.D2, single, complete, average, mcquitty,
median, centroid, kmeans, distance calculation methods:
euclidean, maximum, "manhattan, canberra, binary,
minkowski,indexing methods: kl, ch, hartigan, ccc, scott,
marriot, trcovw, tracew, friedman, rubin, cindex, db,
silhouette, duda, pseudot2, beale, ratkowsky, ball, ptbiserial,
gap, frey, mcclain, gamma, gplus, tau, dunn, hubert, sdindex,
dindex, sdbw, normalization methods: ranked.glsf, global.glsf,
deseq, rpm, spike.in.
Depends: R (>= 3.3.0), ggplot2, plotly
Imports: Matrix, Rtsne, gridExtra, ggpubr, scatterplot3d, RColorBrewer,
knitr, NbClust, reshape, shiny, umap, pheatmap
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
URL: https://github.com/rezakj/iCellR
Suggests: rmarkdown, Rmagic, phateR
NeedsCompilation: no
Packaged: 2019-05-03 21:09:50 UTC; khodaa01
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Hello,
Just checking in. Are you making progress on Martin's suggestion and fixing the warnings/errors? Feel free to message me if you need help with anything.
Hi, I have been very busy lately but I will check them out soon.
Alireza Khodadadi-Jamayran, Senior Bioinformatics Programmer at Applied Bioinformatics Laboratories (ABL) and Genome Technology Center (GTC), Division of Advanced Research Technologies (DART), NYU Langone Medical Center 550 1st Ave, SB-604/MSB-304, New York, NY 10016 E-mail: alireza.khodadadi-jamayran@nyumc.orgmailto:alireza.khodadadi-jamayran@nyumc.org Phone: (212) 263-8132
From: Daniel Van Twisk notifications@github.com Reply-To: Bioconductor/Contributions reply@reply.github.com Date: Thursday, May 16, 2019 at 1:59 PM To: Bioconductor/Contributions Contributions@noreply.github.com Cc: "Khodadadi-Jamayran, Alireza" Alireza.Khodadadi-Jamayran@nyulangone.org, Mention mention@noreply.github.com Subject: Re: [Bioconductor/Contributions] iCellR bioconductor (#1112)
Hello,
Just checking in. Are you making progress on Martin's suggestion and fixing the warnings/errors ?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1112-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAEJUIFFV2BA4BUW5FUDVXZTPVWOG3A5CNFSM4HKXC3FKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVSTBRQ-23issuecomment-2D493170886&d=DwMCaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=YUIcUCslhzSAGdA58ucpqrP8OcYhTe2zaO7rK-YbLqtuZLfYrEziwiD16PiNGltJ&m=Y3_FJ1XaWYNzE7ax2hc7X5rMx6omvcYztgeEMjVJz6k&s=UwyhZnBRomiS_ScQsymajyP61ITX8mPl8uG776oNnbM&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEJUIFHRRSN5H6O7ANDXW33PVWOG3ANCNFSM4HKXC3FA&d=DwMCaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=YUIcUCslhzSAGdA58ucpqrP8OcYhTe2zaO7rK-YbLqtuZLfYrEziwiD16PiNGltJ&m=Y3_FJ1XaWYNzE7ax2hc7X5rMx6omvcYztgeEMjVJz6k&s=e3XGaT1DbxOCBjfOluVYCxs-qznqBK04Tl0IzxYocsE&e=.
Just checking in again since it's been about two weeks. We require that packages that are up for review are actively being worked on. We will need to see activity within the next two weeks of we will need to close the issue. If the issue is closed, it an be reopened at a later time when the developer is ready to work on it again.
Alireza Khodadadi-Jamayran, Senior Bioinformatics Programmer at Applied Bioinformatics Laboratories (ABL) and Genome Technology Center (GTC), Division of Advanced Research Technologies (DART), NYU Langone Medical Center 550 1st Ave, SB-604/MSB-304, New York, NY 10016 E-mail: alireza.khodadadi-jamayran@nyumc.orgmailto:alireza.khodadadi-jamayran@nyumc.org Phone: (212) 263-8132
From: Daniel Van Twisk notifications@github.com Reply-To: Bioconductor/Contributions reply@reply.github.com Date: Wednesday, May 29, 2019 at 1:24 PM To: Bioconductor/Contributions Contributions@noreply.github.com Cc: "Khodadadi-Jamayran, Alireza" Alireza.Khodadadi-Jamayran@nyulangone.org, Mention mention@noreply.github.com Subject: Re: [Bioconductor/Contributions] iCellR bioconductor (#1112)
Just checking in again since it's been about two weeks. We require that packages that are up for review are actively being worked on. We will need to see activity within the next two weeks of we will need to close the issue. If the issue is closed, it an be reopened at a later time when the developer is ready to work on it again.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1112-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAEJUIFDOLDUTOODNQX2UIIDPX232RA5CNFSM4HKXC3FKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWQBSUQ-23issuecomment-2D497031506&d=DwMCaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=YUIcUCslhzSAGdA58ucpqrP8OcYhTe2zaO7rK-YbLqtuZLfYrEziwiD16PiNGltJ&m=uN2LxOqWnYw5814aeXKA_XzM-1X6Au_pBiWh4DNUnzQ&s=j04p97E2JfwH1mstLT2M2blmKAio5tUTY-OwCRjyeUg&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEJUIFE3RIC7HGHTVHSOXWTPX232RANCNFSM4HKXC3FA&d=DwMCaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=YUIcUCslhzSAGdA58ucpqrP8OcYhTe2zaO7rK-YbLqtuZLfYrEziwiD16PiNGltJ&m=uN2LxOqWnYw5814aeXKA_XzM-1X6Au_pBiWh4DNUnzQ&s=_m1xSkovyDQoJweM6vfHN8xfVRv9UQQ539FHer8_Uf4&e=.
Just to clarify, you are saying that you currently do not want the package on Bioconductor? If so, is it okay to close this issue?
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