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After reviewing different tools in ToolShed and discussing with Valentin M., I propose 2 ways of version control:
1. ToolShed controls repository by revision, so for example our PA tool:
* PA revisi…
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Hi Orthograph developers,
I'm trying to get Orthograph to extract orthologous CDS from a target-capture dataset I've generated. I've found a reasonable approach to de novo assemble the captured reg…
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Hi Sebastian,
I really like your tool arriba, it's really fast.
But recently I encountered this weird issue, what's the possible reason for it ? is it because some GTF records ? very similar splic…
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I have a TSV file training_abstracts.tsv when I use the function:
‘def test1():
with open('F:\\small paper\\ner\\data_file\\training_abstracts.tsv', 'r', encoding='utf-8') as f1:
line =…
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Hello,
Should 'multi-organism signaling' be in GO? ('The transfer of information between living organisms.'), but there are no subclasses, and there is a single manual annotation (under dispute). …
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Proteus really needs to have a good way of dealing with proteins and/or peptides that are not detected in one or more of the conditions. Currently, Proteus includes these data int he data import by `l…
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Hi there!
Thanks for developing RawQuant. I feel like it's a really promising tool that will help fixing the "bottleneck" imposed by propietary formats like .RAW in proteomics.
I would like to r…
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Hello,
I tried the -proteinExport function for processing the sample data and found problems in the result. I used the command line `-infile yeast-gold-015-filtered.pia.xml -paramFile parameter.xml -…
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{
"body": {
"sections": {
"section": [
{
"@id": "sec1",
"section-title": "Introduction",
"para": [
{
…
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Hi,
We are currently trying to run a file and it is failing and displaying the following errors:
Executing command:
$> C:\Users\DPCF_SuperComp_v2\Desktop\MSFragger\philosopher-source_windows_a…