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Omics Playground
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Sara Ribeiro
,
Mauro Masiero
2
Aug 23
V3_Genesets upload
Dear User, There is indeed an issue with genesets. We opened an ticket related to this. To give
unread,
V3_Genesets upload
Dear User, There is indeed an issue with genesets. We opened an ticket related to this. To give
Aug 23
marios mat
,
Mauro Masiero
2
Aug 4
Support for bacterial strains
Dear User, We do not have yet support for bacterial species, but that development is in the roadmap.
unread,
Support for bacterial strains
Dear User, We do not have yet support for bacterial species, but that development is in the roadmap.
Aug 4
franp...@hotmail.com
,
Mauro Masiero
2
Jul 13
Error when loading data
Dear User, Thanks for using OmicsPlayground! Could you kindly give more details about this ocurrence,
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Error when loading data
Dear User, Thanks for using OmicsPlayground! Could you kindly give more details about this ocurrence,
Jul 13
BigOmics Analytics Team
,
Ivo Kwee
2
May 22
Question on FDR testing with logFC threshold
Hi Morgane, I think you are referring to the paper "Testing significance relative to a fold-
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Question on FDR testing with logFC threshold
Hi Morgane, I think you are referring to the paper "Testing significance relative to a fold-
May 22
Sara Ribeiro
,
Mauro Masiero
4
May 15
Data upload issue
Perfect, good to hear that it's working! I believe 2.8.17 was one of the last beta test versions,
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Data upload issue
Perfect, good to hear that it's working! I believe 2.8.17 was one of the last beta test versions,
May 15
Andreea C
,
Mauro Masiero
2
May 12
Presenting Proteomics Data
Dear User, Thanks for your message, you could also check the text-based documentation here: https://
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Presenting Proteomics Data
Dear User, Thanks for your message, you could also check the text-based documentation here: https://
May 12
Shahab Mirshahvaladi
,
Mauro Masiero
2
Apr 18
setting the FC cutoff for differential expression analysis
Dear Shahab, Thanks for your suggestion, we are currently not planning in adding this feature, as not
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setting the FC cutoff for differential expression analysis
Dear Shahab, Thanks for your suggestion, we are currently not planning in adding this feature, as not
Apr 18
Ana Contreras
Apr 17
Data upload issue
Hi, I'm trying to upload new data, but I keep getting disconnected. The error message says "
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Data upload issue
Hi, I'm trying to upload new data, but I keep getting disconnected. The error message says "
Apr 17
Shahab Mirshahvaladi
Mar 21
problem in Cluster features in Beta Version
Hi I an not get any images in Cluster features/Gene map (a). There might be a rendering problem in
unread,
problem in Cluster features in Beta Version
Hi I an not get any images in Cluster features/Gene map (a). There might be a rendering problem in
Mar 21
BigOmics Analytics Team
Mar 21
Can analyse the data with setting the organism to Bos taurus?
[Morgane M. email 21.3.2023] Hi, In addition to this first point, I was wondering how I can analyse
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Can analyse the data with setting the organism to Bos taurus?
[Morgane M. email 21.3.2023] Hi, In addition to this first point, I was wondering how I can analyse
Mar 21
BigOmics Analytics Team
Mar 15
Request: keep old heatmap and iTALK in v3
[Shahab email 14.3.3023] The older version had two options for generating heatmaps while the new one
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Request: keep old heatmap and iTALK in v3
[Shahab email 14.3.3023] The older version had two options for generating heatmaps while the new one
Mar 15
Ivo Kwee
Mar 15
New feature request for v3 like Appyter GEO Reverse Search or Set Comparison
[Shahab, email 13.3.2023] the older version had two options for generating heatmaps while the new one
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New feature request for v3 like Appyter GEO Reverse Search or Set Comparison
[Shahab, email 13.3.2023] the older version had two options for generating heatmaps while the new one
Mar 15
BigOmics Analytics Team
3
Mar 10
upload crashes in new version v3beta
resolved. On Friday, 10 March 2023 at 01:00:27 UTC+1 BigOmics Analytics Team wrote: submitted issue
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upload crashes in new version v3beta
resolved. On Friday, 10 March 2023 at 01:00:27 UTC+1 BigOmics Analytics Team wrote: submitted issue
Mar 10
BigOmics Analytics Team
2
Mar 2
celltype identification/deconvolution
Hi Daniel, Celltype estimation/deconvolution is indeed one of the strong functionalities in
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celltype identification/deconvolution
Hi Daniel, Celltype estimation/deconvolution is indeed one of the strong functionalities in
Mar 2
BigOmics Analytics Team
2
Mar 1
How to do best batch correction?
Hi Marian, You're hitting the right questions and answers. It seems your experiments need batch
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How to do best batch correction?
Hi Marian, You're hitting the right questions and answers. It seems your experiments need batch
Mar 1
Mauro Masiero
2
Feb 24
Questions about batch correlation
Thank you for your email! There is no method of choice for batch correction, our approach is to
unread,
Questions about batch correlation
Thank you for your email! There is no method of choice for batch correction, our approach is to
Feb 24
Paul Cantalupo-NV
,
Ivo Kwee
2
Feb 23
Seurat object support
At the moment not directly. You would need to extract the count matrix and metadata (sample
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Seurat object support
At the moment not directly. You would need to extract the count matrix and metadata (sample
Feb 23
Saimul Islam
,
BigOmics Analytics
2
Feb 22
Computation problem
Hey there. Still having problem with this? On Wednesday, December 21, 2022 at 11:54:59 PM UTC+1
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Computation problem
Hey there. Still having problem with this? On Wednesday, December 21, 2022 at 11:54:59 PM UTC+1
Feb 22
Shahab Mirshahvaladi
, …
Staffan Holmqvist
5
Jan 13
isoforms ACs in input file
I am currently working on TMT proteomics analysis. The software does not (to my knowledge!) handle
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isoforms ACs in input file
I am currently working on TMT proteomics analysis. The software does not (to my knowledge!) handle
Jan 13
Staffan Holmqvist
Jan 13
Custom (gene) Families e.g. Differential gene expression
Hi! Thank you for a very slick software. It takes some time to really learn but fantastic after that.
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Custom (gene) Families e.g. Differential gene expression
Hi! Thank you for a very slick software. It takes some time to really learn but fantastic after that.
Jan 13
Staffan Holmqvist
2
10/26/22
Stars and meta.q
Figured this one out. FDR sets the threshold for what q-level each individual test needs to be to
unread,
Stars and meta.q
Figured this one out. FDR sets the threshold for what q-level each individual test needs to be to
10/26/22
Sooheon Kim
10/26/22
Cannot filter samples in clustered heatmap by a certain phenotype
In one of our projects, we have 4 columns defined in samples.csv, and one of these is a binary
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Cannot filter samples in clustered heatmap by a certain phenotype
In one of our projects, we have 4 columns defined in samples.csv, and one of these is a binary
10/26/22
Sooheon Kim
, …
BigOmics Analytics Team
3
10/25/22
Recommended settings for protein data
For proteomics data, I would recommend running T-tests for DE analysis and the Fisher test for GSEA.
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Recommended settings for protein data
For proteomics data, I would recommend running T-tests for DE analysis and the Fisher test for GSEA.
10/25/22
Sooheon Kim
9/21/22
Accessing clustered heatmap gene sets and sample IDs
Hi, I've found some interesting subgroups in the clustered heatmap view, and would like to get
unread,
Accessing clustered heatmap gene sets and sample IDs
Hi, I've found some interesting subgroups in the clustered heatmap view, and would like to get
9/21/22
Shahab Mirshahvaladi
,
BigOmics Analytics Team
2
9/5/22
ordering of top features by SD
Hi. For the unsupervised methods, like the heatmap, you are not allowed to explicitly use any of the
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ordering of top features by SD
Hi. For the unsupervised methods, like the heatmap, you are not allowed to explicitly use any of the
9/5/22
Luís Martins
,
BigOmics Analytics Team
5
8/31/22
some doubts using the platform
Thanks again for your help. I will wait patiently for your input on how the beta features work. Best
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some doubts using the platform
Thanks again for your help. I will wait patiently for your input on how the beta features work. Best
8/31/22
Shahab Mirshahvaladi
8/16/22
Houston, we have a problem!
I am getting disconnected running a list with ~100 DEPs on a local docker. anyone knows a workaround
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Houston, we have a problem!
I am getting disconnected running a list with ~100 DEPs on a local docker. anyone knows a workaround
8/16/22
Ivo Kwee
, …
Felipe da Veiga Leprevost
5
7/27/22
publications on logCPM transformation of MS intensities
Doubt would be a strong word. I have been working with proteomics data analysis for some year now,
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publications on logCPM transformation of MS intensities
Doubt would be a strong word. I have been working with proteomics data analysis for some year now,
7/27/22
Wilson Lwtan
,
BigOmics Analytics
2
6/26/22
Single-cell analysis: Exclude mitochondrial genes / ribosomal genes from highy variable genes prior to dimension reduction
Hi Wilson. I guess this question is best to ask in a forum for scRNAseq, like Seurat. Frequently in
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Single-cell analysis: Exclude mitochondrial genes / ribosomal genes from highy variable genes prior to dimension reduction
Hi Wilson. I guess this question is best to ask in a forum for scRNAseq, like Seurat. Frequently in
6/26/22
Dali Jarboui
,
BigOmics Analytics
2
6/26/22
Proteomics data
Hello! Your correct on all points. Many people have used the Playground successfully for proteomics
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Proteomics data
Hello! Your correct on all points. Many people have used the Playground successfully for proteomics
6/26/22