User: kmyers2

gravatar for kmyers2
kmyers240
Reputation:
40
Status:
New User
Location:
University of Wisconsin-Madison
Twitter:
@unionicola
Last seen:
16 hours ago
Joined:
1 year, 7 months ago
Email:
k******@wisc.edu

Posts by kmyers2

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answer
241
views
1
answers
Comment: C: Analyzing SortMeRNA extracted 16S rRNA
... Thank you! I had no idea these existed!! ...
written 4 months ago by kmyers240
1
vote
1
answer
241
views
1
answer
Analyzing SortMeRNA extracted 16S rRNA
... I am working with someone who has a set of assembled metagenomic data. These data have been assembled into 43 bins. I want to extract the potential 16S rRNA sequences from each bin to try to see if there are any potentially unique genera within these metagenomes. For each bin, I converted the BAM fi ...
de novo assembly 16s sortmerna metagenomics written 4 months ago by kmyers240 • updated 4 months ago by h.mon30k
0
votes
0
answers
158
views
0
answers
Comment: C: Find and Download GenBank File for Whole Genome using Entrez
... Thank you! That file helps a ton! I really appreciate it. ...
written 4 months ago by kmyers240
1
vote
0
answers
158
views
0
answers
Find and Download GenBank File for Whole Genome using Entrez
... I am trying to add an option to a python program I have to allow the user to search and download the Genbank file for the genome of an organism, such as Saccharomyces cerevisiae S288C. I have the following code: handle = Entrez.esearch(db="assembly", term = "Saccharomyces cerevisiae S288C", ret ...
ncbi python entrez genbank biopython written 4 months ago by kmyers240 • updated 3 months ago by Biostar ♦♦ 20
0
votes
1
answer
174
views
1
answers
Comment: C: LexWords perl module for ProDeGe software
... Thank you very much! That's it! ...
written 5 months ago by kmyers240
0
votes
1
answer
174
views
1
answers
Comment: C: LexWords perl module for ProDeGe software
... Thanks. I was afraid of that. ...
written 5 months ago by kmyers240
5
votes
1
answer
174
views
1
answer
LexWords perl module for ProDeGe software
... I am attempting to run our installation of ProDeGe (https://www.nature.com/articles/ismej2015100) but have run up against he following error: Can't locate LexWords.pm in @INC (you may need to install the LexWords module) I have searched for LexWords module in Anaconda (where my perl install is ...
perl installation prodege module lexwords written 5 months ago by kmyers240
1
vote
1
answer
292
views
1
answers
Comment: C: Parsing an ExpressionSet for all SRA addresses
... Wow! Thanks so much. That's exactly what I wanted. It makes sense and I understand better how the ExpressionSet is organized. ...
written 9 months ago by kmyers240
5
votes
1
answer
292
views
1
answer
Parsing an ExpressionSet for all SRA addresses
... I am using GEOquery to download the soft files for a number of experiments from NCBI GEO. For example, here is one individual experiment: > soft <- getGEO('GSE104278', GSEMatrix=T) > soft $GSE104278_series_matrix.txt.gz ExpressionSet (storageMode: lockedEnvironment) ass ...
sra parse expressionset rna-seq R written 9 months ago by kmyers240 • updated 9 months ago by Mark790
1
vote
1
answer
312
views
1
answer
GEOquery with local files
... Is it possible to use GEOquery, specifically the getGEO command, to access matrix files I already have downloaded to my local drive? I am hoping to cut back on the time it takes to download the matrix files. Or is there a way to run getGEO in parallel? ...
ncbi R geoquery geo written 9 months ago by kmyers240 • updated 9 months ago by MatthewP680

Latest awards to kmyers2

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1629 users visited in the last hour