User: biomiha

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biomiha10
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New User
Location:
UK/Cambridge
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3 days, 22 hours ago
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1 year, 2 months ago
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Posts by biomiha

<prev • 16 results • page 1 of 2 • next >
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Comment: C: opencyto Error in .validity_check_alias
... Incidentally, do you still have the gt_080.csv template file anywhere? I'm trying to follow the example here but the link from the tutorials (https://www.dropbox.com/s/jdigjss903q3sgu/gt_080.csv) is broken. Or is that just ICS_080.csv now instead? ...
written 5 weeks ago by biomiha10
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Comment: C: opencyto Error in .validity_check_alias
... Hi Mike, Thanks for your reply and comments. I'll read through the documentation you suggested - I have started collating all the different vignettes, tutorials and templates I can find scattered in various places on the internet. Re your template comment: I just used the templateGen function on a ...
written 5 weeks ago by biomiha10
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Comment: C: Qualifier / getQAStats: Problem to get statisric from a GatingSet
... Yes, that works now. Thanks. ...
written 5 weeks ago by biomiha10
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Comment: C: opencyto Error in .validity_check_alias
... For some reason Dropbox has changed their sharing options and I had to add an email to share the template. I hope it was delivered to the right email address. ...
written 5 weeks ago by biomiha10
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Comment: C: Qualifier / getQAStats: Problem to get statisric from a GatingSet
... Hi Mike, If I try to do the same, I get:  library(QUALIFIER) gs <- load_gs(system.file("/extdata/gs_manual/", package = "flowWorkspaceData")) res <- flowWorkspace::lapply(gs, getQAStats, isMFI = TRUE) Error in data.table(channel = thisChnl, stain = thisStain, stats = names(statsOfNode), ...
written 6 weeks ago by biomiha10
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Comment: C: opencyto Error in .validity_check_alias
... Found this (https://www.bioconductor.org/packages/devel/bioc/vignettes/openCyto/inst/doc/HowToAutoGating.html) so that will be a great place to start re gating methods. Still curious as to how to solve the syntax error. ...
written 6 weeks ago by biomiha10
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opencyto Error in .validity_check_alias
... Hi,   I'm trying to use the OpenCyto platform to streamline our FACS analysis. I've generated a GatingSet from a FlowJo .acs archive - incidentally for other users who've experienced similar problems with .wsp files, I've found that if the workspace is bundled together into an archive then parseWo ...
opencyto written 6 weeks ago by biomiha10 • updated 5 weeks ago by Jiang, Mike1.0k
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Answer: A: TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene
... I would use biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html) ...
written 6 weeks ago by biomiha10
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Comment: C: converting fasta file into bam file
... A BAM file is a binary alignment/map file that holds the information on the sequences from your FASTQ raw output and the coordinates of where they map to. What you need to do now is quantify how many reads map to each transcript or gene. The usual tools for that are Cufflinks or StringTie. Have a lo ...
written 4 months ago by biomiha10
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Comment: C: Converting Exon counts(co-ordinates) to transcript/gene ids
... Why not download transcript level data instead, e.g. from https://jhubiostatistics.shinyapps.io/recount/ ? It's all already been compiled and you can be confident that there aren't any missing exons etc... ...
written 5 months ago by biomiha10

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