Moderator: Bastien Hervé

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Bastien Hervé4.9k
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Karolinska Institutet, Sweden
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Posts by Bastien Hervé

<prev • 829 results • page 1 of 83 • next >
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Comment: C: How to download as table from mycancergenome
... Seems like no option is available for downloading a list of biomarkers. You can still asked them about their API : https://www.mycancergenome.org/content/page/legal-policies-licensing/ ...
written 1 day ago by Bastien Hervé4.9k
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Comment: C: remove mitochondrial reads using Bowtie2
... You cannot do that before alignment, you have to know where a read fits the best before filtering it out or not. For mitochondrial hits you can use `samtools` to remove reads falling into chrM. For all other kind of repeat events, I believe they will be considered as multimapped. Take a look at [sam ...
written 1 day ago by Bastien Hervé4.9k
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Answer: C: DESeq2 problem "DESeqDataSetFromMatrix function"
... What is the output of `library(DESeq2)` ? Is it loading without any error ? ...
written 10 weeks ago by Bastien Hervé4.9k
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Comment: C: problem installing HapMap package in python
... Seems like there is no `HapMap` package on pypi.org https://pypi.org/search/?q=Hapmap Have a look : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040524/ ...
written 10 weeks ago by Bastien Hervé4.9k
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Comment: C: problem installing HapMap package in python
... Try to upgrade pip curl https://bootstrap.pypa.io/get-pip.py | python What are your python and pip version ? https://stackoverflow.com/questions/49748063/pip-install-fails-for-every-package-could-not-find-a-version-that-satisfies https://github.com/tensorflow/tensorflow/issues/39130 ...
written 10 weeks ago by Bastien Hervé4.9k
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Comment: C: Star RNA seq aligner issue:
... We do not have your STAR command line but you can try to reduce the number of thread used and increase the ulimit even more. You can also sort your BAM file afterwards. ...
written 10 weeks ago by Bastien Hervé4.9k
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Comment: C: Star RNA seq aligner issue:
... Did you try what's written in SOLUTION or is it your attempts ? ...
written 11 weeks ago by Bastien Hervé4.9k
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Answer: A: R - Error no 'dimnames' attribute for array
... You can try this : library(Biostrings) sts.data <- c( "TTATAG", "AGATAT", "AGATAG", "ATATCT", "AGATAG", "AGATAG", "AGATAG", "TGATAA", "AGATAA", "AGATAA", "CGATAG", ...
written 3 months ago by Bastien Hervé4.9k
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Comment: C: R - Error no 'dimnames' attribute for array
... You cannot access `A`, `C`, `G`, `T` as you do `seqstatd(seq1)` outputs a list of element, you need to grab the "State frequencies" informations Try to run only these lines : seq1 <- seqdef(seqdecomp(sts.data,sep='')) seqstatd(seq1) t1<-c(A) You will see that `t1` is empty beca ...
written 3 months ago by Bastien Hervé4.9k
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Comment: C: R - Error no 'dimnames' attribute for array
... Are `A`, `C`, `G`, `T` variables or characters : d <-c(A, C, G, T) If they are variables, they are not in your script. If they are characters, you cannot divide characters matrix by float values here : makepssm <-pwm/bg ...
written 3 months ago by Bastien Hervé4.9k

Latest awards to Bastien Hervé

Commentator 13 days ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Scholar 10 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Scholar 3 months ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Scholar 4 months ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Popular Question 4 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Great Question 4 months ago, created a question with more than 5,000 views. For Expression using greek letters in R
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Popular Question 5 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Scholar 5 months ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Popular Question 5 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Appreciated 5 months ago, created a post with more than 5 votes. For C: Python or R
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Popular Question 7 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Great Question 10 months ago, created a question with more than 5,000 views. For Fastest way to subset dataframe in python
Popular Question 11 months ago, created a question with more than 1,000 views. For ChIP-Seq experiment, MACS2 bdgpeakcall 0 fold-change, pvalue and qvalue
Popular Question 11 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Popular Question 13 months ago, created a question with more than 1,000 views. For Apply Deseq2 size factor to aligned reads
Popular Question 14 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
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Scholar 19 months ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python

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