Moderator: igor

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igor11k
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Posts by igor

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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... I cannot recall any particular publication. A lot of pathways (for example MSigDB C2) are based on a single study. Although I do not doubt that many are reliable, we also know that many are not reproducible. Additionally, even in a well-executed study, most genes are usually not validated, either i ...
written 20 days ago by igor11k
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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... > blog entry on the subject is interesting, and mentions how far-away organisms may behave worse It seems one of their conclusions is that the C2 gene sets are substantially more reliable than the well-curated Hallmark ones which is highly counter-intuitive. ...
written 20 days ago by igor11k
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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... > using enrichment analysis is kind of...not reliable Some would argues that is the case even for the same species, but that would be an entirely separate topic. ...
written 20 days ago by igor11k
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Comment: C: CellRanger with CITE-seq and hashing
... > it's not supported by 10x Cell Ranger can handle CITE-seq and hashtags. Seurat has a vignette on this topic: https://satijalab.org/seurat/v3.2/multimodal_vignette.html ...
written 20 days ago by igor11k
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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... The MSigDB gene sets use human genes. However, many are based on mouse and rat studies (check the "organism" field for the individual gene sets). These were then converted to human symbols by the MSigDB team, so they consider the pathways to be sufficiently similar across those species. ...
written 21 days ago by igor11k
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Comment: C: Why it is not use UMIs for RNA-seq?
... > UMIs are necessary for scRNA They are preferable, but not necessary. Some scRNA-seq methods do not use UMIs. ...
written 23 days ago by igor11k
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Comment: C: Any alternatives to Cellranger aligner that Seurat can read?
... Seurat has a function (Read10X) to make it easier to read Cell Ranger output. It converts that output to a matrix. You don't have to use that function. CreateSeuratObject() requires a standard R matrix. ...
written 4 weeks ago by igor11k
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Comment: C: Did TCGA consortium recommend any best practice guideline for cross-sample RNAse
... There is some additional discussion about TCGA normalization and that table specifically here: https://www.biostars.org/p/357870/ ...
written 4 weeks ago by igor11k
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Comment: C: LoFreq input file issues
... Have you checked the [documentation][1] where it describes the necessary inputs? [1]: http://csb5.github.io/lofreq/commands/ ...
written 5 weeks ago by igor11k
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Comment: C: Should discodant alignments be retained in ChIP-Seq experiments?
... Do discordant alignments exist in those tutorials? Usually, ChIP-seq experiments are single-read (not paired-end) so that is not an option. ...
written 6 weeks ago by igor11k

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