Comments (8)
Hi @alexvpickering ,
Thanks for the issue.
We are still working on this, in the meantime, I will share a workable version soon.
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Status update: I'm creating some test data for 0.14 so I can bring in Avi's code into tximport
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Thanks for this report. We’ll take a look. @k3yavi and I have a meeting already for tomorrow to discuss the next iteration of the Alevin file format. And we can figure out how tximport needs to change to accommodate Salmon 0.14.
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Hi @alexvpickering ,
Thanks again for raising the issue. As requested by one other user too, we have a shared a basic (non-optimized) R parser for the alevin 0.14.0 output in this COMBINE-lab/salmon#380 thread. We are still working on optimizing the parser and integrating it with tximport
and will update you once it is stable.
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I’ve got a little code but didn’t finish today and want to put in a unit test alongside the new code.
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Thanks for notifying us quickly to this issue.
Should be fixed by 6f761a7
You can obtain the new code with install_github("mikelove/tximport")
. If you can test that it works on your end, i'll push it to release as well.
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I just pushed 1.12.2 to release branch as well, so it gets circulated tomorrow
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Thanks @mikelove !
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Related Issues (20)
- Outdated vignette? HOT 1
- Move Alevin import code to C++ HOT 3
- Missing release tags HOT 1
- Add option to import only whitelisted barcodes from alevin HOT 2
- ignoreAfterBar does not apply with txOut=T and countsFromAbundance != "no" HOT 1
- lose transcript names for salmon inferential replicates
- `ignoreAfterBar` not used if `txOut=TRUE` HOT 5
- cann't import kallisto abundance.h5/.tsv HOT 4
- Import processed data HOT 3
- Recomended count scaling method for DTU analysis HOT 2
- Returns TPM when abundanceCol is set to any value for type='rsem' HOT 1
- Read in files in parallel HOT 4
- Tximport issue with new R version HOT 2
- Which measure to use for gene Fold change analysis between pre- and post-treatment samples and for gene comparison within a sample HOT 1
- error in 1:nrow(m): argument of length 0 HOT 1
- import using tximport for the rsem count table to get integers? HOT 3
- Dealing with multispecies using tximport HOT 4
- Different length and counts depending on the number of loaded samples HOT 1
- tximport of feature counts? HOT 1
- tximport of kallisto h5s generated with multiple threads is not deterministic HOT 1
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