-
I tried computing tumor abundance (in terms of TPM, transcript per million) using kallisto, and my result looks very different compared with the result posted at https://doi.org/10.1016/j.cell.2020.09…
-
Hi,
I have 2 questions:
1- Is there a better documantion of the output files?
2- In the "neoantigens/sample1/Class_II/" diretory the following files are missing:
sample1_MHC_Class_I_all_epi…
-
can I select the neoantigen by the order of pvacseq output.
for example ,
Median MT Score; Median WT Score ;Median Fold Change
should I select by the Median Fold Change?
and the percentile rank i…
-
Hi there, I'm just reading through the github and want to make sure I'm not misinterpreting the different modules. We have already used mutect2 and a few other somatic callers on our aligned files and…
-
Hi,
I am running the entire nextNEOpi pipeline on the TESLA dataset https://doi.org/10.1016/j.cell.2020.09.015 Currently, I'm experiencing issues with pVACsec for data from patient1, specifically som…
-
Hi,
I met a problem that there is no output results for some of my samples. The error message shows:
```
Making Immunogenicity prediction
(None, 256)
Making Neoantigen Filtering
usage: seq2neo…
-
Hello @ibn-salem @priesgo @ozlemmuslu @martinloewer @mostafiz2010
I'm having some problems with Easyfuse. At first, the test data is ok, and get results. But there is a problem in the Step Fetchd…
-
* pvactools version: 3.1.1
* Python version: 3.7 (from pVACtools docker hub image)
* Operating System: Debian 10 (from pVACtools docker hub image)
**Describe the bug**
When using NNAlign predict…
-
Hi authors,
Thanks for MSFragger. But I get the following error when trying to run MSFragger on my Mac (M1 pro, Ventura 13.3):
`java -jar MSFragger-3.7.jar open_fragger.params_edited data/W_N18/…
-
Greetings,
Thank you for providing this open source tool. I have been using the default setting of casanovo for most of my proteomics denovo analysis. Recently, I was interested to determine the su…