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**Describe the bug**
I used the agat_sp_compare_two_annotations.pl script to compare the reference GTF with the predicted GTF of the full-length transcriptome with a view to obtaining differences in …
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Hi, How to interpret positive and negative scores for genes? I mean if I have five genes with score (-2,-1,0,1,2), which are the two top scores, ie, (1,2) or (-2,2)? Thanks for your help.
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When downloading this file ('iatlas-ici-features.tsv') from the Synapse portal it's not given in the description what the meaning of the columns are.
There seem to be columns linked to various stu…
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Are you interested in getting involved in Project Cognoma? If so, introduce yourself here.
I'll begin. I'm [Daniel Himmelstein](http://dhimmel.com/), a Postdoctoral Fellow in the [Greene Lab](http://…
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We need to work out how to manage somatic classifications.
Eg How is it different from current germline ACMG in terms of scoring and evidence keys?
Dumping out notes here:
### Comment 1 ###
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R:
write.csv(df_bulk, file = "df_bulk.csv", quote = FALSE, row.names = TRUE)
python:
p = PUREE()
purities_and_logs = p.get_output(dir_dataset.joinpath("df_bulk.csv"), 'HGNC')
![image](https…
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Hello
thanks for devolving the neofox alogirhtem. I am trying to build a singularity container and then test the data sets. However, i can't figure out why the test data failed. Can you help to ch…
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Hi,
Thanks for developing this good method to predict tumor purity. May I ask where I can get the gene symbols used in your method, especially for your 158 biomarkers? I want to confirm that my gene…
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Hello,
I'm not sure at what stage STAR-fusion fails - but it seems to have generated the star-fusion.fusion_predictions.abridged.coding_effect.tsv but might be missing some of the output files fro…
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Hello, thank you for this amazing tool. I have predicted annotations using GeMoMa v1.9 in red oak genome using the reference genome annotation and wanted to compare both the annotation. For that purpo…