User: wd

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wd10
Reputation:
10
Status:
New User
Location:
Germany
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3 days, 16 hours ago
Joined:
2 years, 7 months ago
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Posts by wd

<prev • 17 results • page 1 of 2 • next >
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Comment: C: differential expression analysis of htseq data with edgeR/voom
... Thank you Aaron and James for your explanations/help. Much Appreciated! ...
written 3 days ago by wd10
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height boxes gene models GeneRegionTrack Gviz
... Hi I created two GeneRegionTracks with Gviz, one for genes on the plus strand, and one for genes on the minus strand. gffTrack_PLUS<- GeneRegionTrack(txdb_PLUS, chromosome=scaffold,from=st, to=en,showId=TRUE,utr3="#FFD58A",utr5="#FFD58A", background.title="transparent",fontcolor.group="#808080" ...
gviz generegiontrack stack written 5 days ago by wd10
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Comment: C: R Gviz ideogram custom track
... Thank you, that worked! ...
written 10 days ago by wd10
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R Gviz ideogram custom track
... Hi I tried the suggestions here to create an Ideogram fora scaffold my custom genome, but I can't make it work. My bands dataframe (bands.txt) looks like this: chrom chromStart chromEnd name gieStain scaffold_1 1 7801961 test1 gpos25 scaffold_10 ...
ideogram gviz R track custom genome written 11 days ago by wd10
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differential expression analysis of htseq data with edgeR/voom
... Dear all I 'm trying to run a differential expression analysis with edgeR/voom (combining guidelines from https://www.bioconductor.org/help/workflows/RNAseq123/  and http://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html) and using count tables from 10 RNAseq samples (5 "EXP" (treatment) s ...
limma edger voom htseq rnaseq123 written 4 months ago by wd10 • updated 4 months ago by Aaron Lun16k
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Answer: A: outlier detection of RNAseq samples
... Dear Fabian, Ryan, Michael and Peter Thank you for your valuable advice! Very much appreciated. Kind regards Wannes   ...
written 10 months ago by wd10
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outlier detection of RNAseq samples
... Hi I have RNA seq data for six different treatments (A,B,C,D,E,F) of a model organism, with four-fold biological (NOT technical) replicates. FASTQC revealed no abnormalites in the RNAseq data and after normalization (rlogtransformation) with DESeq2 I generated a PCA plot (using the 500 most variab ...
rnaseq deseq2 outlier pca hierarchical clustering written 10 months ago by wd10
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extractUpstreamSeqs with custom genome, no gene_id shown
... Hi I'm trying to use extractUpstreamSeqs from the GenomicsFeatures package with a custom genome using the following commands: txdb <- makeTxDbFromGFF("test.gff3",format="gff3") genome<-FaFile("test_genome.fasta", index=sprintf("%s.fai", "test_genome.fasta")) open(genome) promoter_transcript ...
featureextraction genomicfeatures genomicranges txdb written 18 months ago by wd10 • updated 18 months ago by Martin Morgan ♦♦ 20k
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Comment: C: calculate total transcript length from DisjointExons output (Genomic Ranges Obje
... Thank you, that worked! ...
written 18 months ago by wd10
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Comment: C: calculate total transcript length from DisjointExons output (Genomic Ranges Obje
... Thank you Michael for the quick reply. However, I would like to have the exonic length of every gene, but excluding overlap of exons with neighbouring genes. Wannes ...
written 18 months ago by wd10

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