mbourgey / scrna_gbm Goto Github PK
View Code? Open in Web Editor NEWanalysis script for GBM single cell RNA seq data
scrna_gbm's People
Contributors
Stargazers
Watchers
scrna_gbm's Issues
BT400.bam and bai files permissions are not correct so they can be downloaded.
Please modify the BT400.bam file permissions so that the file can be downloaded from the website in the readme. Thanks!
Metadata Missing
Hi @mbourgey ,
I am trying to use your data in my analysis, I read the paper and I didn't see the metadata such as cell types "OLC, GPC, Neuronal, Astrocytic, Mesenchymal,Classical"
Would you mind if you provide this data to us?
duplication in cellranger data
I think the 2 components for BT364 are duplicates. This is after importing the cellranger data from the link in the README.md.
> allr[12:13]
$`filtered/BT364_1of2.filtered_gene_matrices`
class: SingleCellExperiment
dim: 33694 3665
metadata(1): Samples
assays(1): counts
rownames(33694): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
ENSG00000268674
rowData names(2): ID Symbol
colnames: NULL
colData names(2): Sample Barcode
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
$`filtered/BT364_2of2.filtered_gene_matrices`
class: SingleCellExperiment
dim: 33694 3665
metadata(1): Samples
assays(1): counts
rownames(33694): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
ENSG00000268674
rowData names(2): ID Symbol
colnames: NULL
colData names(2): Sample Barcode
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
> assay(allr[[12]][1:4,1:4])
4 x 4 sparse Matrix of class "dgCMatrix"
ENSG00000243485 . . . .
ENSG00000237613 . . . .
ENSG00000186092 . . . .
ENSG00000238009 . . . .
> library(sparseMatrixStats); colSums(assay(allr[[12]][,1:4]))
1/0 packages newly attached/loaded, see sessionInfo() for details.
[1] 14972 5804 4804 10336
> library(sparseMatrixStats); colSums(assay(allr[[13]][,1:4]))
0/0 packages newly attached/loaded, see sessionInfo() for details.
[1] 14972 5804 4804 10336
A query about normal cell types
Hello,
Woudl you mind providing cell labels of normal cells from HFA*_cd133/total and NSC1_cd133 data please (labels like tRG, uRG, IPC as shown in your Fig2a)?
I appreciate for your help!
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.