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HI Chuiqin,
I met a problem like below when I run your tutorial, could you help me debug this issue? Thanks a ton!
> irGSEA.density.scatterplot(object = pbmc3k.final, method = "UCell", show.geneset …
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Dear developers,
I love the clusterprofiler package and it simplifies my workflow for downstream analysis of clusters from single-cell data tremendously. I mainly use the gseGO and gseKEGG function…
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Currently, the seed database (on database schema 2.6.0), contains the MSigDB gene sets. This is useful for testing validation and loading of test study `study_es_0`, as well as potentially loading any…
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Hi~
Recently I have realized that there is a more hidden parameters called `maxGSSize`, which really influence the result of enricher/GSEA analysis. According to the raw code in DOSE，I think it may…
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Hi authors,
I saw it in the paper that you are using positional gene sets, motif gene sets and immunological signatures as features. I wonder how you put three dataset into one list. Additionally, …
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Would it be possible to include the "exact source" field to the output of `getMsigdb`? In most cases, these are more standard identifiers than the uppercase names provided by the MSigDB. For example, …
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Do you have any recommendations for visualising the output of test_gene_overrepresentation?
Can it/should it use a clusterprofiler viz method: https://yulab-smu.github.io/clusterProfiler-book/ or a…
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Hello members,
I am currently working with TPM expression data obtained from RNA-seq analysis, and my dataset includes a diverse range of biotypes such as miRNA, lncRNA, pseudogenes, etc., resultin…
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Hi
Any help for this error
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Hello!
I've been trying to run gseapy on a cluster after installing via conda environment.
Whenever I give gp.prerank multiple genesets to examine, as:
["KEGG_2019_Mouse","MSigDB_Hallmark_20…