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Shahab Mirshahvaladi
,
Mauro Masiero
3
11/16/23
setting the FC cutoff for differential expression analysis
Thanks Mauro. I saw the conversation in github. sounds good. On Tuesday, April 18, 2023 at 7:45:53 PM
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setting the FC cutoff for differential expression analysis
Thanks Mauro. I saw the conversation in github. sounds good. On Tuesday, April 18, 2023 at 7:45:53 PM
11/16/23
Sara Ribeiro
,
Mauro Masiero
2
8/23/23
V3_Genesets upload
Dear User, There is indeed an issue with genesets. We opened an ticket related to this. To give
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V3_Genesets upload
Dear User, There is indeed an issue with genesets. We opened an ticket related to this. To give
8/23/23
marios mat
,
Mauro Masiero
2
8/4/23
Support for bacterial strains
Dear User, We do not have yet support for bacterial species, but that development is in the roadmap.
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Support for bacterial strains
Dear User, We do not have yet support for bacterial species, but that development is in the roadmap.
8/4/23
franp...@hotmail.com
,
Mauro Masiero
2
7/13/23
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,
7/13/23
BigOmics Analytics Team
,
Ivo Kwee
2
5/22/23
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-
5/22/23
Sara Ribeiro
,
Mauro Masiero
4
5/15/23
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,
5/15/23
Andreea C
,
Mauro Masiero
2
5/12/23
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://
5/12/23
Ana Contreras
4/17/23
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 "
4/17/23
Shahab Mirshahvaladi
3/21/23
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
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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
3/21/23
BigOmics Analytics Team
3/21/23
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
3/21/23
BigOmics Analytics Team
3/15/23
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
3/15/23
Ivo Kwee
3/15/23
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
3/15/23
BigOmics Analytics Team
3
3/10/23
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
3/10/23
BigOmics Analytics Team
2
3/2/23
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
3/2/23
BigOmics Analytics Team
2
3/1/23
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
3/1/23
Mauro Masiero
2
2/24/23
Questions about batch correlation
Thank you for your email! There is no method of choice for batch correction, our approach is to
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Questions about batch correlation
Thank you for your email! There is no method of choice for batch correction, our approach is to
2/24/23
Paul Cantalupo-NV
,
Ivo Kwee
2
2/23/23
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
2/23/23
Saimul Islam
,
BigOmics Analytics
2
2/22/23
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
2/22/23
Shahab Mirshahvaladi
, …
Staffan Holmqvist
5
1/13/23
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
1/13/23
Staffan Holmqvist
1/13/23
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.
1/13/23
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
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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
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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