User: wd

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wd10
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Location:
Germany
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1 week ago
Joined:
3 years, 9 months ago
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Posts by wd

<prev • 19 results • page 1 of 2 • next >
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Comment: C: DESEq2 comparison with two conditions and paired experiments
... Dear Prof. Love Thank you for your reply. I guess I'll have to perform more downstream experiments whether the DEGs of the ad-hoc procedure are meaningful. Just to give you an idea: this is a gene that is not significantly downregulated (based on FDR) according to the recommend test (test of inter ...
written 10 days ago by wd10
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Comment: C: DESEq2 comparison with two conditions and paired experiments
... Hi I have a similar setup of experiments (but with experiments not being paired) I have two genotypes (geno): "A","B", Two treatments (treat): "control" "damage" Four replicates for each genotype/treatment combination, 16 samples in total I want to know whether the effect of "damage" compared to ...
written 10 days ago by wd10
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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 14 months 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 14 months ago by wd10
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Comment: C: R Gviz ideogram custom track
... Thank you, that worked! ...
written 14 months 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 14 months 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 18 months ago by wd10 • updated 18 months ago by Aaron Lun21k
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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 2.0 years 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 2.0 years 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 2.7 years ago by wd10 • updated 2.7 years ago by Martin Morgan ♦♦ 22k

Latest awards to wd

Popular Question 18 months ago, created a question with more than 1,000 views. For outlier detection of RNAseq samples
Popular Question 18 months ago, created a question with more than 1,000 views. For ape - delete bootstrap values (node.labels) less than a certain value

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