User: Matthew Thornton

Reputation:
300
Status:
Trusted
Location:
USA, Los Angeles, USC
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
6 years, 7 months ago
Email:
m***************@med.usc.edu

Posts by Matthew Thornton

<prev • 45 results • page 1 of 5 • next >
0
votes
2
answers
41
views
2
answers
Answer: A: Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differi
... Hello! I had to contact Alex Pico on github and this is the solution that he developed for me. What a cool guy! Thanks for the thorough bug report. Yes, you've correctly identified the problem: CyREST (and therefore RCy3) does not handle node attributes of type list at this time. The current functi ...
written 7 days ago by Matthew Thornton300
0
votes
2
answers
41
views
2
answers
Comment: C: Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differi
... It doesn't work with the whole graph either. ...
written 9 days ago by Matthew Thornton300
0
votes
2
answers
41
views
2
answers
Comment: C: Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differi
... It doesn't work with the whole graph either. ...
written 9 days ago by Matthew Thornton300
0
votes
2
answers
41
views
2
answers
Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
... Hello! I am trying to subset and import a graphNEL of GO terms made using the 'GOstats' package into Cytoscape using the 'RCy3' package and it isn't working. The data comes from the output of the 'termGraphs' function of GOstats library(GOstats) ## from the vignette params1 <- new ...
rgraphviz gostats cytoscape rcy3 written 9 days ago by Matthew Thornton300
0
votes
1
answer
81
views
1
answers
Comment: C: Combining and using 10x Genomics output in SingleCellExperiment Objects
... Thanks! That was very helpful! ...
written 6 weeks ago by Matthew Thornton300
1
vote
1
answer
81
views
1
answer
Combining and using 10x Genomics output in SingleCellExperiment Objects
... Hello! I am trying to get used to the new 'SingleCellExperiment' objects. Specifically how to rename samples and add metadata, swap out Ensembl IDs for Gene Names. For example, If I read in my 10x genomics data using 'DropletUtils' i have to specify a path to the data which is then incorporated i ...
singlecellexperiment written 6 weeks ago by Matthew Thornton300 • updated 6 weeks ago by Aaron Lun23k
0
votes
2
answers
88
views
2
answers
Answer: A: Segmentation Fault with development versions of R, Bioconductor, and DropletUtil
... ulimit was the issue. I assumed that it was unlimited, but when I checked it was 8145, so I changed it to 65536 and it worked. Thank you! ...
written 6 weeks ago by Matthew Thornton300
1
vote
2
answers
88
views
2
answers
Segmentation Fault with development versions of R, Bioconductor, and DropletUtils when processing output of CellRanger 3.0.2
... Hello! I have the output of the latest CellRanger software 3.0.2. I was unable to load the molecule_info.h5 file with the released version of DropletUtils. I was told that I needed to use the development version of DropletUtils for newer cellranger output. So I installed a development version of ...
bioc-devel dropletutils written 6 weeks ago by Matthew Thornton300
0
votes
1
answer
73
views
1
answers
Comment: C: Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into Drople
... Hello! I am using the development version of DropletUtils and It is loading the data, but now I am getting a segfault with the downsampling. It is only using one core for the downsampling even though it uses the BiocParallel library. Here is my error: > tmp <- "/home/met/data/Hong_Lab/ ...
written 7 weeks ago by Matthew Thornton300
0
votes
1
answer
73
views
1
answers
Comment: C: Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into Drople
... Hello! I just saw in a previous answer that I will have to use the development version of DropletUtils with the CellRanger 3.0.2 output. ...
written 7 weeks ago by Matthew Thornton300

Latest awards to Matthew Thornton

Popular Question 2.6 years ago, created a question with more than 1,000 views. For Importing RMA processed data into limma for eBayes
Great Question 2.6 years ago, created a question with more than 5,000 views. For Limma design and contrast matrix question.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For What is the easiest way to make the GC content and length matrix for package cqn?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Limma design and contrast matrix question.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 294 users visited in the last hour