Dear all, please may I ask for a suggestion regarding the algorithms to cluster the expression data in single cells (scRNA-seq) at multiple time points : we do have expression data for 30 000 genes in 10 datasets that have been collected at multiple time points, and i was wondering if you could please recommend *any algorithms/R packages that could help with the clustering of the gene expression at different time points.* thanks a lot, and all the best, -- bogdan
algorithms that cluster time series data
4 messages · Sarah Goslee, Bogdan Tanasa, Bert Gunter
Hi, Unsupervised classification (clustering) is a huge field. There's an entire task view devoted to it, where you can see many of the large array of R packages that perform some sort of clustering. https://cran.r-project.org/web/views/Cluster.html Since that is an overwhelming list, you may be best served by looking at how others in your field have approached similar problems, and then look for R packages that perform the relevant analyses. Sarah
On Mon, Jul 6, 2020 at 1:11 PM Bogdan Tanasa <tanasa at gmail.com> wrote:
Dear all,
please may I ask for a suggestion regarding the algorithms to cluster the
expression data in single cells (scRNA-seq) at multiple time points :
we do have expression data for 30 000 genes in 10 datasets that have been
collected at multiple time points,
and i was wondering if you could please recommend *any algorithms/R
packages that could help with the clustering of the gene expression at
different time points.* thanks a lot, and all the best,
-- bogdan
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Sarah Goslee (she/her) http://www.numberwright.com
Dear Sarah, thank you very much for pointing to the list of available packages and algorithms.
On Mon, Jul 6, 2020 at 10:20 AM Sarah Goslee <sarah.goslee at gmail.com> wrote:
Hi, Unsupervised classification (clustering) is a huge field. There's an entire task view devoted to it, where you can see many of the large array of R packages that perform some sort of clustering. https://cran.r-project.org/web/views/Cluster.html Since that is an overwhelming list, you may be best served by looking at how others in your field have approached similar problems, and then look for R packages that perform the relevant analyses. Sarah On Mon, Jul 6, 2020 at 1:11 PM Bogdan Tanasa <tanasa at gmail.com> wrote:
Dear all, please may I ask for a suggestion regarding the algorithms to cluster the expression data in single cells (scRNA-seq) at multiple time points : we do have expression data for 30 000 genes in 10 datasets that have
been
collected at multiple time points,
and i was wondering if you could please recommend *any algorithms/R
packages that could help with the clustering of the gene expression at
different time points.* thanks a lot, and all the best,
-- bogdan
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sarah Goslee (she/her) http://www.numberwright.com
And since this is about RNA expression data, you would do better posting on the Bioconductor Help site rather than here. You are more likely to find the expertise and interest you seek there. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Mon, Jul 6, 2020 at 10:22 AM Sarah Goslee <sarah.goslee at gmail.com> wrote:
Hi, Unsupervised classification (clustering) is a huge field. There's an entire task view devoted to it, where you can see many of the large array of R packages that perform some sort of clustering. https://cran.r-project.org/web/views/Cluster.html Since that is an overwhelming list, you may be best served by looking at how others in your field have approached similar problems, and then look for R packages that perform the relevant analyses. Sarah On Mon, Jul 6, 2020 at 1:11 PM Bogdan Tanasa <tanasa at gmail.com> wrote:
Dear all, please may I ask for a suggestion regarding the algorithms to cluster the expression data in single cells (scRNA-seq) at multiple time points : we do have expression data for 30 000 genes in 10 datasets that have
been
collected at multiple time points,
and i was wondering if you could please recommend *any algorithms/R
packages that could help with the clustering of the gene expression at
different time points.* thanks a lot, and all the best,
-- bogdan
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sarah Goslee (she/her) http://www.numberwright.com ______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.