greenleaflab / 10x-scatac-2019 Goto Github PK
View Code? Open in Web Editor NEWPublication Page for Satpathy*, Granja* et al 2019
Publication Page for Satpathy*, Granja* et al 2019
Hi,
Thanks for your great works and sharing your code. When I use your analyze the umap trajectory code to construct the trajectory in my own data, I have some questions. Hope you can help me figure out.
I feel a little confused that if I have no idea the development background in my data, how can I choose the clusters to build the trajectory? In the paper, you extract the B cell associated cluster to reverse reconstruction of B cell differentiation trajectory. I wanna know can I use the unsupervised methods to learn the trajectory.
Some specific questions for your code, how you choose the latest cluster? And which matrix contain the delta ATAC number between each cluster?
Thanks a lot.
Thank you very much for the inspiring publication. We are wondering if it'd be possible that you can share cluster identity, cell barcode and peak count matrix corresponding to the Fig 5a. In your shared data it seems to be lacking them. It would be very much appreciated.
Best,
Rong
fragments <- fragments[mcols(fragments)[,by] %in% rownames(tssSingles)[tssSingles$cellCall==1]]
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘NSBS’ for signature ‘"standardGeneric"’
Hi, I'm an ArchR user that was directed to this repository to perform CNV Analysis since the feature is not yet available in ArchR.
I have a few questions about how this repository works. I see that the work is transferred from step to step via RDS files, so since CNV analysis is the 8th step, I will have to do some number of steps before. Which are necessary?
Another question I have is how to input multiple fragment files. I noticed that a list of vector paths, like in ArchR, doesn't work on the first step, though a single file path does. Is there a way to do this with multiple files?
Thanks!
Hugo Kitano
Hi,
I am rerunning your human-mouse cell mixture data, but I cannot find a proper list to use for gene.ranges and tss.ranges. Could you share with me how you find a proper list for the human and mouse genes when you analysis by Signac?
Thank you so much!
Z
Hi,
Thanks for sharing the code.
But I couldn't find code about 'TF footprinting analysis' from the available scripts. Since I couldn't tell some detail about this part just from paper, I would really appreciate it if you are willing to share with us.
Best,
Huan
Hello,
It's really an awsome wroking. But I got a error by using your workflow in 01_Filter_Cells_v2, as following:
fragments <- fragments[mcols(fragments)[,by] %in% rownames(tssSingles)[tssSingles$cellCall==1]]
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘NSBS’ for signature ‘"standardGeneric"’
I don't know the ### mcols(fragments)[,by] meaning, and I got error in this formula.
Hope you could help me out.
Thanks
Making Seurat LSI Object...
Binarizing matrix...
Getting top 20000 features...
Computing Term Frequency IDF...
Computing SVD using irlba...
Making Seurat Object...
Error in CreateSeuratObject(mat, project = "scATAC", min.cells = 0, min.genes = 0) :
unused argument (min.genes = 0)
Was just wondering if someone might be able to comment on what changes would be needed to adapt the 05_Cluster_Unique_Peaks_v2.R script to make it appropriate for detecting unique gene activities, rather than using peaks.
From a review of the script and the methods section of the manuscript, it seems like at changing the 1st argument of the uniqueFeatures()
function from:
edgeR::cpm(assay(sePB),log=TRUE,prior.count=3)
to
log2(edgeR::cpm(2^assay(sePB)-1) +1)
would be required.
Similarly, it seemed like it may be necessary to change the lines 144, 175, 185, 254, and 263 in the createPseudoBulk()
function, to first convert back to gene activity scores and then log transform, however I wasn't sure about that.
Would be great to hear anyones thoughts on those changes and any others that might be required to work with gene activities rather than peaks.
Thanks in advance!
Do you have the file just like this ? This is the Cicero hematopoiesis datasets from your work. The author of paper "Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity" said that we can obtain Cicero PBMC dataset by contacting to you. Look forward your reply!
Hi,
I really appreciate your work on scATAC-seq.
I tried to run GWAS chromVAR on single-cell summarized experiment using co-accessibility. However, I was unable to find the dataset of PICS_GWAS_SNPS.gr.rds.
Would it be possible to provide this data?
Thank you so much!
Hi,
I have downloaded scATAC_Heme_All_SummarizedExperiment.final.rds followed your links.
I checked the Group
information in colData
. And I also want to use the segments files from this cells.
table(Heme_meta_info$Group)
B_Cells BM_pDC Bone_Marrow_Rep1
2982 162 6011
CD34_Progenitors_Rep1 CD34_Progenitors_Rep2 CD4_HelperT
10056 4764 1413
CLP CMP Dendritic_Cells
92 585 1265
GMP HSC LMPP
471 349 90
Memory_CD4_T_Cells_Rep1 Memory_CD4_T_Cells_Rep2 Memory_CD8_T_Cells
1206 1416 1089
MEP Monocytes MPP
181 1868 146
Naive_CD4_T_Cells_Rep1 Naive_CD4_T_Cells_Rep2 Naive_CD8_T_Cells
625 1888 1945
NK_Cells PBMC_Rep1 PBMC_Rep2
1110 9616 6163
PBMC_Rep3 PBMC_Rep4 Regulatory_T_Cells
4847 944 2598
I could find most of them from GSE129785_RAW.tar in GSE129785.
But I also need segmants files of CLP, CMP, GMP, HSC, LMPP, MEP and MPP
which I guessed from your CELL PAPER Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.
But there weren't paired segmants submiited in GSE96769.
Can you re-submitted segments files of the Hematopoiesis cells on GEO datasets again or other ways?
Thanks a lot.
Good day!
I am currently using ArchR. Great package! However, there is no implementation of CNA there (maybe in the future?). I have generated the cnaObj based on the code you shared. However, I am not sure how to plot the results. Could you please share how to do it and generate a nice figure like the one in your publication?
Thanks in advance!
Hi,
I am trying to access some public data from your paper and I followed the instructions of "Getting 10x scATAC-seq Bam Files" in README. In the final figure of README, the bam file link is downloadable but as you can see below there isn't any downloadable link for the bam file. I also tried to get bam files using AWS but it didn't work.
I only need to have access to the following bam files;
If you can point me to the files or guide me how to get them, I'll really appreciate.
Many thanks,
Ravza
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.