User: dlmatera

gravatar for dlmatera
dlmatera10
Reputation:
10
Status:
New User
Location:
Last seen:
13 hours ago
Joined:
7 months ago
Email:
d*******@umich.edu

Posts by dlmatera

<prev • 11 results • page 1 of 2 • next >
0
votes
0
answers
94
views
0
answers
Comment: A: How to determine SC-RNA-SEQ QC filter thresholds in Seurat?
... any additional advice? edit: my general problem is that the various online resources all seem to pick an arbitrary threshold for QC (Specifically for the minimum features metric), whereas there seems to be more resources for mitochondrial QC and doublet detection, etc. ...
written 2 days ago by dlmatera10
0
votes
0
answers
94
views
0
answers
Comment: C: How to determine SC-RNA-SEQ QC filter thresholds in Seurat?
... What is shown in the image was simply VlnPlots after creating a Seurat object with the raw GEO data, no QC or normalization applied yet. This was from a 10X platform, but I cannot give any information on pre-processing that was done by the researchers, etc. - here is the omnibus link that I fetch ...
written 5 days ago by dlmatera10
2
votes
0
answers
94
views
0
answers
How to determine SC-RNA-SEQ QC filter thresholds in Seurat?
... Is there a more definitive way to decide on QC cutoffs for SC-RNA-SEQ? I understand low read counts (incomplete capture of the cell) and high read counts (potential doublet/multiplet) are an issue, but I've seen a lot of variation in the thresholds used throughout all of the different learning mater ...
R rna-seq seurat written 6 days ago by dlmatera10
0
votes
3
answers
276
views
3
answers
Comment: A: Easiest way to homogenize gene aliases across datasets?
... Hi all! Thanks for the help I think I have got this working. However, some have recommended I find a way to check if the results or accurate (or do something more advanced than a find& replace because this could introduce errors?) Does anyone have some recommendations? I manually checked the res ...
written 6 days ago by dlmatera10 • updated 6 days ago by GenoMax94k
0
votes
3
answers
276
views
3
answers
Comment: A: Easiest way to homogenize gene aliases across datasets?
... Ok so I downloaded the HGNC dataset (thanks to all who helped me find this) and reorganized my data, now I have List #1- All features (gene names..aliases and official) from my dataset in one column. List #2 -official gene names from HGNC (column 1) an aliase (column 2) Im currently trying to fin ...
written 6 weeks ago by dlmatera10
0
votes
3
answers
276
views
3
answers
Comment: C: Easiest way to homogenize gene aliases across datasets?
... im curious if there's an easy way to automate this? ...
written 6 weeks ago by dlmatera10
0
votes
3
answers
276
views
3
answers
Comment: C: Easiest way to homogenize gene aliases across datasets?
... yep gene symbols, not sure if they are all the official HGNC one ...
written 6 weeks ago by dlmatera10
0
votes
3
answers
276
views
3
answers
Comment: C: Easiest way to homogenize gene aliases across datasets?
... all human gene symbols, for example one is SELENOW (dataset#1), SELW (dataset#2), and SEPW1 (dataset #3) ...
written 6 weeks ago by dlmatera10
11
votes
3
answers
276
views
6 follow
3
answers
Easiest way to homogenize gene aliases across datasets?
... I've got 3 rna seq datasets Im trying to integrate and there are ~1000genes with different aliases across sets (when I integrate them these genes do not merge appropriately as the Seurat package assumes these different aliases are in fact different genes) Is there any easy way to go about homogeni ...
gene R alignment rna-seq written 6 weeks ago by dlmatera10
0
votes
0
answers
131
views
0
answers
Whats the easiest way to make and quantify gene-drug-pathway interaction network?
... Nodes would be significantly altered genes and pathways, and the drugs of interest. Im trying to narrow down a large list of drugs by quantifying how many differentially expressed pathways and genes they modulate. Im also curious what the best statistical test is to see if drugs "significantly" mo ...
gene R rna-seq written 6 months ago by dlmatera10

Latest awards to dlmatera

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: 1535 users visited in the last hour
_