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Forum: RNA Sequencing 11-04-2016, 03:32 PM
Replies: 45
Views: 24,453
Posted By axa9070
For me it was Name, but this thread was very...

For me it was Name, but this thread was very helpful.
Forum: Bioinformatics 05-25-2016, 02:11 PM
Replies: 0
Views: 1,256
Posted By axa9070
Post GeneTrail 2

I've really started liking this tool called GeneTrail 2 (https://genetrail2.bioinf.uni-sb.de/). There is a REST API for it and I'd like to take full advantage of it in R. There is already a client...
Forum: Illumina/Solexa 06-06-2015, 08:07 AM
Replies: 7
Views: 4,884
Posted By axa9070
What does PHRED stand for?

I know it seems like a silly question to ask, but Google has no answer for me, nor do the papers published by Phil Green and Brent Ewing themselves. The wikipedia article...
Forum: Bioinformatics 11-03-2014, 01:35 PM
Replies: 46
Views: 17,379
Posted By axa9070
Thanks Loyal! We appreciate your time and...

Thanks Loyal!

We appreciate your time and hard work!

^_^
Forum: Bioinformatics 11-03-2014, 01:03 PM
Replies: 2
Views: 2,846
Posted By axa9070
hey stephenhart: Would you mind posting this...

hey stephenhart:
Would you mind posting this function's output:


> head(features(myGene))
seqnames start end width strand source type score phase
1 1 12442003 12442535 ...
Forum: Bioinformatics 11-03-2014, 12:50 PM
Replies: 2
Views: 2,846
Posted By axa9070
stephenhart: I have the first issue but not that...

stephenhart: I have the first issue but not that second one.

Either way, does anyone have any ideas yet?


Using EMBL annotation:

> cuff <- readCufflinks(genome="vinifera.fa",...
Forum: RNA Sequencing 10-30-2014, 03:26 PM
Replies: 89
Views: 42,124
Posted By axa9070
This site...

This site (http://stackoverflow.com/questions/13524053/installing-libcurl-and-non-root-user-need-to-configure-where-code-looks-for-lib) might help. I ended up needing to install curl for my Debian...
Forum: Bioinformatics 10-30-2014, 11:16 AM
Replies: 46
Views: 17,379
Posted By axa9070
Solution

You CAN have your cake and eat it too!

The latest RSQLite has deprecated the sqliteQuickSQL function! However, has been essentially renamed to dbGetQuery! So by simply loading the cummeRbund...
Forum: Bioinformatics 10-30-2014, 09:39 AM
Replies: 46
Views: 17,379
Posted By axa9070
Nevermind. This way of finding it was totally...

Nevermind. This way of finding it was totally janky! (If you look at the packages off of these links you'll know what I mean http://cran.fhcrc.org/bin/windows/contrib/)
But the old windows binaries...
Forum: Bioinformatics 10-30-2014, 09:29 AM
Replies: 46
Views: 17,379
Posted By axa9070
So basically what you're saying is that...

So basically what you're saying is that cummeRbund does not work with the updated RSQLite package.

Probably because (whether by mistake or not) RSQLite 1.0.0 does not have the sqliteQuickSQL...
Forum: Bioinformatics 10-27-2014, 09:33 AM
Replies: 46
Views: 17,379
Posted By axa9070
I'm having the exact same problem =[ Error...

I'm having the exact same problem =[

Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n--...
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