User: adrija.kalvisa

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Posts by adrija.kalvisa

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ChicagoTools fitDistCurve.R: how to fit p-value weights when comparing two treatments?
... I am trying to estimate the p-value weight settings by using ChicagoTools `fitDistCurve.R` using replicates from my own samples as an input. I want to compare two treatments (three replicates per treatment), however, I am not sure whether I should calculate a separate weight adjustment for each tre ...
pchi-c R bioconductor chicago written 4 months ago by adrija.kalvisa0 • updated 4 months ago by a11msp110
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Comment: C: estimating read length and SD for Kallisto (single-end QuantSeq reads)
... Hi Michael, just a question: do you need to supply the insert size or the fragment size for Kallisto quant in single end mode? I think Kallisto documentation mentions that the input of -l should be 'fragment sizes'. ...
written 4 months ago by adrija.kalvisa0
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Where did 'antisense' biotype go when transitioning from mm9 to mm10 genome build in encode?
... I have been comparing GTF annotations for mm9 and mm10 genome builds from ensembl and noticed that several biotypes are unique for mm9 and mm10 gtf files. **transcript_biotype for mm10 (but not for mm9):** IG_C_pseudogene, IG_D_pseudogene, IG_LV_gene, IG_pseudogene, IG_V_pseudogene, lncRNA, non_st ...
mm9 mm10 gtf ensembl written 5 months ago by adrija.kalvisa0 • updated 5 months ago by ATpoint34k
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Meaning of columns in Chicdiff::chicdiffPipeline() output *_results.Rmd
... What is the content of Chicdiff::chicdiffPipeline() output from *_results.Rmd? I am currently following a tutorial on differential interaction calling (https://github.com/RegulatoryGenomicsGroup/chicdiff) and The column names of this output are the following: [1] group [2] baseMean [3] log2Fold ...
pchi-c capture hi-c chicdiff R written 5 months ago by adrija.kalvisa0 • updated 4 months ago by Biostar ♦♦ 20

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