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hi kristoffer,
I am getting an error during step 3 of isoformSwitchAnalysisPart 1() :
`Step 1 of 3 : Detecting isoform switches... Step 2 of 3 : Adding and predicting open reading frames Step …
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Hello,
We are trying to analyze isoform switches between two groups (n ≈ 500 samples total), for ≈5,000 isoforms from ≈2,000 genes. However, we have encountered some difficulties in running the `i…
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Hi,
I tried running the quick analysis and ran into this Error during isoformSwitchAnalysisPart1.
`Step 1 of 3 : Detecting isoform switches...
Step 2 of 3 : Adding and predicting open reading …
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Dear SUPPA developers,
first of all: thanks a lot for providing your nice tool set!
I have one feature suggestion though:
Since you have now included a script for the differential analysis of s…
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Hi there,
I imported data from Stringtie using importRdata, then successfully ran IsoformSwitchAnalysisPart1, followed by IsoformSwitchTestDEXSeq, on my SwitchList. The problem is that my results r…
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This is not urgent, but something I noticed that you might want to be aware of. I ran `extractConsequenceSummary` with `returnResults = TRUE` and it reported zero genes or isoforms for "Intron struct…
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Hi,
Thank you for this excellent package for analyzing isoform switching, but I encounter a problem.
This program seems very slow that it is impossible to finish:
I do not know what's the problem.…
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I recently compared the top isoform hits from IsoformSwitchAnalyzeR from reads that were aligned using two different methods: 1) RSEM/STAR and 2) Salmon. In both cases isoformSwitchAnalysisPart1 was f…
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Hi. I'm having some issues (and confusion) in relation to the arguments for designmatrix and comparisonstomake.
I can import the kallisto data with:
`Txi_trans_F
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Hi @amykglen,
I'm wondering if we can keep the longest description from one of the preferred curies' synonyms in KG2C. Here is an example:
For the curie `CHEMBL.COMPOUND:CHEMBL1199307` in KG2C …