User: holgerbrandl

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holgerbrandl30
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Posts by holgerbrandl

<prev • 9 results • page 1 of 1 • next >
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Answer: A: BigWig library for Java
... There is a bigwig library for Kotlin https://github.com/JetBrains-Research/big which runs on the JVM. And since kotlin can be used from Java (see https://kotlinlang.org/docs/reference/java-to-kotlin-interop.html) it might be an option for you. ...
written 8 months ago by holgerbrandl30
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Should cndas provided by Ensembl be filtered by ccds or biotype prior to running kallisto?
... I typically download cdnas directly from Ensembl (like with `wget ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz`), build a `kallisto index`, and run `kallisto quant` to estimate isoform abundance. However, Ensembl tends to provide very detailed tran ...
isoforms kallisto written 9 months ago by holgerbrandl30
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Comment: C: Why are DESeq2 size factors not null in case of sparse count matrix?
... Indeed, genes with no counts in even only one sample are excluded. I obtain the **exactly** same factors as provided by DESeq2 when adopting my implementation from above to include such a filtering step: size_factors = dataLong %>% group_by(ensembl_gene_id) %>% fil ...
written 17 months ago by holgerbrandl30
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Comment: C: Why are DESeq2 size factors not null in case of sparse count matrix?
... Indeed, when excluding all 0 counts from the data, I get factors that come very close to what DESeq2 is providing. Somehow this tiny but important details seems to be left out very often when explaining size-factor normalization. Some examples: # A tibble: 36 x 3 sample size_fac ...
written 17 months ago by holgerbrandl30
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Comment: C: Why are DESeq2 size factors not null in case of sparse count matrix?
... Thanks for detailing out the definition again. I've tried to implement exactly this protocol in my code from above. To illustrate the problem better, I've updated the example data to become a sparse count matrix, which results in following size factors sample size_fac 1 sa ...
written 17 months ago by holgerbrandl30
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Why are DESeq2 size factors not null in case of sparse count matrix?
... Hi, I've followed the vignette to just perform size factorn normalization using DESeqDataSetFromMatrix(countData = countMatrix, colData = colData, design = ~ 1) dds = estimateSizeFactors(dds) sizeFactors(dds) I've read the docs of `DESeq2::estimateSizeFactors` but I still struggle ho ...
deseq2 deseq rna-seq written 17 months ago by holgerbrandl30 • updated 17 months ago by Kevin Blighe45k
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Comment: C: TPM or FPKM as input values for PCA and WGCNA?
... What is the mean expressed transcript length? What is the meaning of "dependence" in this context? Why are FPKMs more "dependent" than TPMs which also take length into account? ...
written 19 months ago by holgerbrandl30
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Answer: A: How To Convert Bed Format To Gtf?
... Alliteratively you could convert bed to gtf using [this][1] [kscript][2]let: kscript https://git.io/vbJ4B my.bed > my.gtf [1]: https://github.com/holgerbrandl/kutils/blob/master/tools/genomic_coordinates/bed2gtf.kts [2]: https://github.com/holgerbrandl/kscript ...
written 19 months ago by holgerbrandl30
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Answer: A: Show Progress (Bar?) For Blast+ Query
... Here's a kotlin solution using [kscript][1]. The logic to estimate the progress is similar to the other solutions but it's shorter and more portable (since it java-based). blast_progress(){ kscript - $* <<"EOF" //DEPS de.mpicbg.scicomp:kutils:0.3 //KOTLIN_OPTS -J-Xmx5g ...
written 2.8 years ago by holgerbrandl30

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