User: just

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just0
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Posts by just

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Comment: A: miRNA-seq data analysis
... Thanks for the reply. Differential expression will come next. Ideally, it would be nice to have a tool starting from scratches (alignment, quantification etc). Any ideas? ...
written 8 months ago by just0
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miRNA-seq data analysis
... I would like to analyze microRNA sequencing data. However I'm lacking the experience here. Which pipeline would you recommend? The idea would be at the end to combine this data with TCGA dataset Thank you for your help! ...
mirna mirna-seq written 8 months ago by just0 • updated 8 months ago by Jon Bråte130
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Gviz and gene annotation tracks (error on a chromosome level Tracklist)
... Hey guys, my idea is to plot custom annotation of the regions (microRNAs and promoters) as well as Ensembl annotations of the protein-coding genes. I did the following: # annotation for microRNA mir_track <- AnnotationTrack(microrna_range, id="miR-150", genome="GRCh37", name="miR-150",         ...
gviz written 15 months ago by just0 • updated 15 months ago by Johannes Rainer1.0k
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Answer: A: Gviz - adding ensembl gene annotation track
... Thank you for your help, guys!  This is what worked for me in the end: library(Gviz) library(EnsDb.Hsapiens.v75) edb <- EnsDb.Hsapiens.v75 gr <- getGeneRegionTrackForGviz(edb, filter = GenebiotypeFilter("protein_coding"), chromosome="chr19", start=start,                                 end ...
written 15 months ago by just0
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Gviz - adding ensembl gene annotation track
... Hey guys, I'm trying to plot genomic locus of interest. I'd be particularly interested in protein-coding genes. I've thought about loading Ensembl track using ensGenes2 <- UcscTrack(genome = "hg19", chromosome = "chr19",                       track = "ensGene", from = start, to = end, trackType ...
gviz ensembl written 15 months ago by just0
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Gviz ploting of annotation for H3K4me3 and H3Kme1 from UCSC
... Hey guys, I'm trying to load an annotation track from UCSC for H3K4me3 and H3Kme1 into gviz. I used this H3K4me3_H1ESC <- UcscTrack(track ="wgEncodeRegMarkH3k4me3", table = "wgEncodeBroadHistoneH1hescH3k4me3StdSig", trackType="AnnotationTrack",                          genome='hg19', chromosom ...
gviz ucsc written 20 months ago by just0 • updated 20 months ago by Robert Ivanek350

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