IsoformSwitchAnalyzeR

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Welcome to the IsoformSwitchAnalyzeR google group where people can ask questions or report bugs.

If you report a bug/error please specify which version of IsoformSwitchAnalyzeR you are using and repport all the code which gave the problem.

Feel free to help me help others if you know the answer :-)

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Xingliang Zhu

Jan 16

Is there any example about how to input stringtie mapping result into IsoformSwitchAnlayzeR?

Hi, Is there any example about how to input stringtie long reads mapping result into

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Is there any example about how to input stringtie mapping result into IsoformSwitchAnlayzeR?

Hi, Is there any example about how to input stringtie long reads mapping result into

Jan 16

John Smout

12/30/23

switchPlot() does not show all isoforms

Hi, Follow up question to my previous question. As mentioned before, I'm using

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switchPlot() does not show all isoforms

Hi, Follow up question to my previous question. As mentioned before, I'm using

12/30/23

John Smout

12/22/23

Large discrepancy between estimated and detected DTU

Hi all, I'm working on a small dataset (8 samples, 3 treatments) and trying to look at

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Large discrepancy between estimated and detected DTU

Hi all, I'm working on a small dataset (8 samples, 3 treatments) and trying to look at

12/22/23

Katrin Moller

12/20/23

Help importing data

Hi there, I have a dataset produced by Nanopore sequencing. Due to my lack of knowledge in processing

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Help importing data

Hi there, I have a dataset produced by Nanopore sequencing. Due to my lack of knowledge in processing

12/20/23

Laura López Hernández, Eric Katagirya2

12/19/23

Error using importRdata

Were you able to solve this? I have the same error with my analysis. I even repeated the Salmon

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Error using importRdata

Were you able to solve this? I have the same error with my analysis. I even repeated the Salmon

12/19/23

Majd Abdulghani

10/9/23

missing part of figure

Hello, I plotted the consequence enrichment plot as follows: subsettedList, consequencesToAnalyze=

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missing part of figure

Hello, I plotted the consequence enrichment plot as follows: subsettedList, consequencesToAnalyze=

10/9/23

Majd Abdulghani, Kristoffer Vitting-Seerup4

9/23/23

StringTie readLength when using long reads

Hi again Kristoffer, Sorry, can you please explain which part of the analysis will be affected by the

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StringTie readLength when using long reads

Hi again Kristoffer, Sorry, can you please explain which part of the analysis will be affected by the

9/23/23

sumitra sivaprakasam

9/21/23

Error in converting strintie gene id using IsoformSwitchAnalyzeR

Hi everyone, I've been trying to perform hisat2-stringtie analysis for my bacterial genome. I

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Error in converting strintie gene id using IsoformSwitchAnalyzeR

Hi everyone, I've been trying to perform hisat2-stringtie analysis for my bacterial genome. I

9/21/23

Majd Abdulghani, Kristoffer Vitting-Seerup3

9/19/23

Subsetting specific comparisons

Gotcha. I did this and it worked: subsettedList <- subsetSwitchAnalyzeRlist( switchAnalyzeRlist =

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Subsetting specific comparisons

Gotcha. I did this and it worked: subsettedList <- subsetSwitchAnalyzeRlist( switchAnalyzeRlist =

9/19/23

Majd Abdulghani, Kristoffer Vitting-Seerup9

9/13/23

no signal peptides found

In case someone else ran into the same issue: the output from SignalP 5.0 worked. Just don't use

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no signal peptides found

In case someone else ran into the same issue: the output from SignalP 5.0 worked. Just don't use

9/13/23

Victoria J

9/6/23

Step 1 of 2: importing GTF (this may take a while)... Error in `$<-.data.frame`(`*tmp*`, "geneType", value = NA) : replacement has 1 row, data has 0

Hello, I have been struggling with adding annotated ORFs to my switchAnalyzeRlist. The annotations I

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Step 1 of 2: importing GTF (this may take a while)... Error in `$<-.data.frame`(`*tmp*`, "geneType", value = NA) : replacement has 1 row, data has 0

Hello, I have been struggling with adding annotated ORFs to my switchAnalyzeRlist. The annotations I

9/6/23

pshtiwan babane

9/3/23

Error "no repilcate to estimate"

Hello Everyone after updating isoformswitchAnalzerR Package, i got this error and my design includes

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Error "no repilcate to estimate"

Hello Everyone after updating isoformswitchAnalzerR Package, i got this error and my design includes

9/3/23

noorus...@gmail.com

8/25/23

Usage of Alternate Open Reading Frame

Hi Kristoffer, I previously used your IsformSwitchAnalyzeR for detecting isoform switching but I

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Usage of Alternate Open Reading Frame

Hi Kristoffer, I previously used your IsformSwitchAnalyzeR for detecting isoform switching but I

8/25/23

Caleb, Kristoffer Vitting-Seerup4

8/3/23

Import R data error: 'X' Contains Missing Values

I managed to get it to run by catenating the FASTQ files from the same KD biological replicate so

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Import R data error: 'X' Contains Missing Values

I managed to get it to run by catenating the FASTQ files from the same KD biological replicate so

8/3/23

Serigne Basse

7/10/23

No signial peptides were found

Hi, Y have an error with the Part2 my code is: exampleSwitchList <- isoformSwitchAnalysisPart2(

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No signial peptides were found

Hi, Y have an error with the Part2 my code is: exampleSwitchList <- isoformSwitchAnalysisPart2(

7/10/23

Harshangda Karan Puri, Kristoffer Vitting-Seerup2

6/26/23

event ratio correction and cell number correction

IsoformSwitchAnalyzeR will use generalized linear modeling to handle this, meaning it will just

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event ratio correction and cell number correction

IsoformSwitchAnalyzeR will use generalized linear modeling to handle this, meaning it will just

6/26/23

Tainã Cardoso, Kristoffer Vitting-Seerup3

6/15/23

remove isoform from the ASwitchAnalyzelist

I performed a filter based on the expression in other tissues.... getting only isoforms that I

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remove isoform from the ASwitchAnalyzelist

I performed a filter based on the expression in other tissues.... getting only isoforms that I

6/15/23

Megan Noonan, Kristoffer Vitting-Seerup2

5/17/23

Error in dplyr::left_join(transcriptData, orfData, by = "isoform_id"

Yes. An update of dplyr causes this problem. Grap the latest version from GitHub and that will fix

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Error in dplyr::left_join(transcriptData, orfData, by = "isoform_id"

Yes. An update of dplyr causes this problem. Grap the latest version from GitHub and that will fix

5/17/23

Aman Akash2

4/19/23

unused argument (dIFcutoff = 0.3)

Okay, by digging some more, I think I was following an older manual of IsoformSwitchAnalyzer which

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unused argument (dIFcutoff = 0.3)

Okay, by digging some more, I think I was following an older manual of IsoformSwitchAnalyzer which

4/19/23

Caleb, Kristoffer Vitting-Seerup2

4/12/23

No overlap between annotation and quantification

My guess is that your fasta file ( Homo_Sapiens.GRCh38.cdna.all.fa.gz ) does not contain the

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No overlap between annotation and quantification

My guess is that your fasta file ( Homo_Sapiens.GRCh38.cdna.all.fa.gz ) does not contain the

4/12/23

Caleb, … Kristoffer Vitting-Seerup7

4/11/23

Problem with dplyr during addORFfromGTF

Just follow the installation instructions on github :-) torsdag den 6. april 2023 kl. 16.29.35 UTC+2

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Problem with dplyr during addORFfromGTF

Just follow the installation instructions on github :-) torsdag den 6. april 2023 kl. 16.29.35 UTC+2

4/11/23

kris r, Kristoffer Vitting-Seerup3

3/20/23

isoformSwitchAnalysisPart1 error satuRn

Looks like your previous post...? fredag den 17. marts 2023 kl. 21.57.06 UTC+1 skrev kris r: Hello, I

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isoformSwitchAnalysisPart1 error satuRn

Looks like your previous post...? fredag den 17. marts 2023 kl. 21.57.06 UTC+1 skrev kris r: Hello, I

3/20/23

lu lu, Kristoffer Vitting-Seerup9

3/17/23

Error in h(simpleError(msg, call)) isoformSwitchAnalysisPart1

Thanks for sharing your data Lu! :-) fredag den 17. marts 2023 kl. 14.26.07 UTC+1 skrev Kristoffer

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Error in h(simpleError(msg, call)) isoformSwitchAnalysisPart1

Thanks for sharing your data Lu! :-) fredag den 17. marts 2023 kl. 14.26.07 UTC+1 skrev Kristoffer

3/17/23

kris r, Kristoffer Vitting-Seerup2

3/15/23

aSwitchList error

You just need to upgrade to the newest version from github :-) tirsdag den 14. marts 2023 kl. 21.45.

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aSwitchList error

You just need to upgrade to the newest version from github :-) tirsdag den 14. marts 2023 kl. 21.45.

3/15/23

Betül Bozkurt, … Kristoffer Vitting-Seerup7

3/13/23

Runtime: isoformSwitchAnalysisCombined()

Sure Kristoffer, I opened an issue about the error on github few minutes ago. Thank you! 13 Mart 2023

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Runtime: isoformSwitchAnalysisCombined()

Sure Kristoffer, I opened an issue about the error on github few minutes ago. Thank you! 13 Mart 2023

3/13/23

lu lu

3/9/23

Importing Data from Salmon via Tximeta + isoformSwitchAnalysisPart1 get error 'pathToGTF' argument

Hey Kristoffer, I imported my Data from Salmon via Tximeta, then used isoformSwitchAnalysisPart1, but

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Importing Data from Salmon via Tximeta + isoformSwitchAnalysisPart1 get error 'pathToGTF' argument

Hey Kristoffer, I imported my Data from Salmon via Tximeta, then used isoformSwitchAnalysisPart1, but

3/9/23

Harshangda Karan Puri, Kristoffer Vitting-Seerup2

3/2/23

Error in importRData

Please don't cross-post problems. I answered on GitHub. onsdag den 1. marts 2023 kl. 17.25.05 UTC

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Error in importRData

Please don't cross-post problems. I answered on GitHub. onsdag den 1. marts 2023 kl. 17.25.05 UTC

3/2/23

Harshangda Karan Puri, Kristoffer Vitting-Seerup8

3/1/23

Error in `dplyr::full_join() while using importRdata

Hi, Thanks! I needed to upgrade DESeq2. So this is resolved. Harsha On Wednesday, March 1, 2023 at 7:

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Error in `dplyr::full_join() while using importRdata

Hi, Thanks! I needed to upgrade DESeq2. So this is resolved. Harsha On Wednesday, March 1, 2023 at 7:

3/1/23

Анастасия Васильева, Kristoffer Vitting-Seerup3

1/30/23

addORFfromGTF NA in orfAnalysis columns

Did you solve this problem? Else I can say the one with NA (called MSTAG*) are the once you found

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addORFfromGTF NA in orfAnalysis columns

Did you solve this problem? Else I can say the one with NA (called MSTAG*) are the once you found

1/30/23

AHMED ALARABI, Kristoffer Vitting-Seerup5

12/16/22

switchPlot() figures issue!

Unfortunately, such an example is not possible as that depends on how you (and other people) run

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switchPlot() figures issue!

Unfortunately, such an example is not possible as that depends on how you (and other people) run

12/16/22