search

dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
267 stars 98 forks source link

Can we use SingleR to annotate BulkRNAseq when reference is also bulk #156

Closed Rohit-Satyam closed 10 months ago

Rohit-Satyam commented 10 months ago

Hi @zhihua-chen @dtm2451 @LTLA

I was wondering if I can use SingleR package to transfer labels from a time series Bulk RNAseq to another bulk RNASeq? We want to check (for QC purpose only) to which time point the query Bulk RNASeq belongs to (we know the time point at which cells were synchronized but we want to be sure)?

Rohit-Satyam commented 10 months ago

We have time-series dataset (reference with two replicates per time point) and between each time point is the 2hr difference. in the past, we have successfully used this dataset to see which timepoints our single cells were synchronized at and the label transferred matches with the phenotype data we have from the imaging.

This time i got some bulk rnaseq samples with drug treatment and was asked to see if say 8hrs samples look-like 6hr samples or below based on expression data. A simple method would be to subset reference dataset first for genes expressed in this new query dataset, order the rows, and perform pairwise correlation of both the dataframes using corbetw2mat function to get pairwise-correlation coefficient. But I wanted to use something reliable like singleR which would derive a set of marker genes!!

dtm2451 commented 10 months ago

I think the bioconductor version of SingleR (bioc, github) should work fine for this purpose.

I also need to note that you've posted this as an issue on the legacy version of Singler, from before SingleR was updated for bioconductor. There are some extra constraints to using this legacy version of the package, owing in large part to distinct data structure requirements. There are also differences in features, and the version here does not benefit from the many efficiency improvements that @LTLA has implemented in the bioconductor version.

We highly recommend using the bioconductor version, which also happens to be the only version that Aaron and I can provide effective support for. If you are using that version, please make issues over here.

Rohit-Satyam commented 10 months ago

Hi @dtm2451

Yes I am using Bioc version. Thanks for confirming that singleR can be used.