User: cook.675

gravatar for cook.675
cook.67510
Reputation:
10
Status:
New User
Location:
Last seen:
8 hours ago
Joined:
1 month ago
Email:
c*******@gmail.com

Posts by cook.675

<prev • 35 results • page 1 of 4 • next >
0
votes
0
answers
56
views
0
answers
Comment: C: PCA plot interpretation from scRNA data set
... Thanks so much I will try these things! ...
written 7 hours ago by cook.67510
0
votes
0
answers
56
views
0
answers
Comment: C: PCA plot interpretation from scRNA data set
... With regard to point 2, this is not the case when we look at a list of DEG by cluster. We see a wide range of effect on genes within the clusters that we would expect biologically with treatment. about point 1), the implication there is that this is because the cells form two groups on the PC plot ...
written 13 hours ago by cook.67510
0
votes
0
answers
56
views
0
answers
PCA plot interpretation from scRNA data set
... Hi we are working on a scRNA data set that is a population of cells that has either been treated with control (VEH) or with treatment (IMQ) and I had some questions about the understanding of PCA; We ran the PC analysis for the integrated dataset and plotted PC1 vs PC2, grouped by stimulation and w ...
pca scrna seq seurat written 15 hours ago by cook.67510
0
votes
0
answers
66
views
0
answers
Comment: C: Summing data from 3 different parts of an R object at once
... guys I got it!!! X <- sum(Object$orig.ident == "V1" & Object$"Phase" == "G1" & Object$"seurat_clusters" == 0) ...
written 2 days ago by cook.67510
1
vote
0
answers
66
views
0
answers
Summing data from 3 different parts of an R object at once
... I have 3 replicate samples from a scRNA seq experiment; call them V1, V2, V3. I merged them into one large object "Object". When I merged them I appended the replicate name to the column barcodes, for example V2_ATGGAGTGGAT etc... Object has a meta data column for cell cycle state located at `Objec ...
R scrna seq seurat written 3 days ago by cook.67510
0
votes
0
answers
115
views
0
answers
Comment: C: subsetting matrix elements and creating a histogram
... Ahhh yes I have it now! Thank you so much ...
written 3 days ago by cook.67510
0
votes
0
answers
115
views
0
answers
Comment: C: subsetting matrix elements and creating a histogram
... Thanks; I only have access to the data set I ran on 6000 cells now, so the matrix is 24 x 6000 but its the same thing essentially. The histogram shows one giant bar at frequency 6000 and then some smaller ones. Summary(x) shows: Min. 1st Qu. Median Mean 3rd Qu. Max. 12.0 55 ...
written 4 days ago by cook.67510
0
votes
0
answers
115
views
0
answers
Comment: C: subsetting matrix elements and creating a histogram
... Here if we just look at the first data point in the vector it has x[1] CGATGGCTCGCACTCT 1 How would you separate out the number from the string? ...
written 7 days ago by cook.67510
0
votes
0
answers
115
views
0
answers
Comment: C: subsetting matrix elements and creating a histogram
... It seems im having some trouble understanding this data structure: When I make `x <- colSums(Umi.adt)` x is a vector of type double, but it seems to have 2 dimensions, one is the tags, and the other is the sums that we calculated previously. When I do `attributes (x)` I get..... $names [1] " ...
written 7 days ago by cook.67510
0
votes
0
answers
115
views
0
answers
subsetting matrix elements and creating a histogram
... I have some data from CITEseq experiment (Umi.adt) I want to look at. The matrix is 24 x 200000 where the rows are antibody names and the columns are barcodes (cells). Many of the cells have few, little to no UMI counts. I want to make a histogram with frequency on the y axis, and UMI count on the ...
rna-seq written 7 days ago by cook.67510 • updated 7 days ago by RamRS24k

Latest awards to cook.675

Scholar 4 weeks ago, created an answer that has been accepted. For A: How to remove entire rows from seurat object based on cellhash read

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 752 users visited in the last hour