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Omics Playground
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Omics Playground
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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
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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
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
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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
Sarah Sczelecki
,
BigOmics Analytics
2
6/24/22
Disconnected
Hi Sara. First, please try to pull the newest docker. We recently fixed a bug. If you still get
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Disconnected
Hi Sara. First, please try to pull the newest docker. We recently fixed a bug. If you still get
6/24/22
Vikram Subramanian
,
BigOmics Analytics
2
6/24/22
Understanding file types
Hi Vikram. BigOmics Playground need your original raw data (counts, intensities). Your file contains
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Understanding file types
Hi Vikram. BigOmics Playground need your original raw data (counts, intensities). Your file contains
6/24/22
Ivo Kwee
2
6/24/22
Compare two more datasets
There are different ways you can do it 1. Merging the data sets, then assess for batch effects and if
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Compare two more datasets
There are different ways you can do it 1. Merging the data sets, then assess for batch effects and if
6/24/22
Gavin Bewick
,
Ivo Kwee
2
3/9/22
upload counts
Best is the raw counts (if you have) if you use edgeR and DEseq2 algorithms. If you supply normalised
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upload counts
Best is the raw counts (if you have) if you use edgeR and DEseq2 algorithms. If you supply normalised
3/9/22
Thorben Sauer
10/25/21
Rendering Issue Heatmap
Hey guys, I think I observed an issue with the heatmap rendering function. In the left dendogram, I
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Rendering Issue Heatmap
Hey guys, I think I observed an issue with the heatmap rendering function. In the left dendogram, I
10/25/21
BigOmics Analytics Team
,
Thorben Sauer
4
9/7/21
post-hoc test, ANOVA
Hi Thorben. It's confusing because (I think) there are two types of "multiple testing"
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post-hoc test, ANOVA
Hi Thorben. It's confusing because (I think) there are two types of "multiple testing"
9/7/21
Matthias Kirsch
, …
Ivo Kwee
3
9/2/21
docker on windows gets stuck
Hi Matthias. I checked the latest docker image, and the CSV fiiles from the example.zip file should
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docker on windows gets stuck
Hi Matthias. I checked the latest docker image, and the CSV fiiles from the example.zip file should
9/2/21
Eduardo Beltrame
,
BigOmics Analytics Team
2
8/31/21
How to save a session with a locally uploaded dataset?
Hi Eduardo. Are you using the docker version or one of our public servers (public.bigomics.ch or
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How to save a session with a locally uploaded dataset?
Hi Eduardo. Are you using the docker version or one of our public servers (public.bigomics.ch or
8/31/21
BigOmics Analytics Team
2
8/31/21
correlation method of cluster annotation
We use the Spearman's rank correlation for the calculation which is calculated as the Pearsons
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correlation method of cluster annotation
We use the Spearman's rank correlation for the calculation which is calculated as the Pearsons
8/31/21
Ivo Kwee
,
BigOmics Analytics Team
2
8/31/21
Correction of meta-q value
Great question. In Omics Playground, the multiple test correction is done before q-value aggregation.
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Correction of meta-q value
Great question. In Omics Playground, the multiple test correction is done before q-value aggregation.
8/31/21