User: a.james

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a.james120
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120
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Germany
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15 hours ago
Joined:
4 years, 3 months ago
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a******@dkfz-heidelberg.de

Posts by a.james

<prev • 58 results • page 1 of 6 • next >
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CWL to check the output directory and run for non-existing files
... Hello All, I have a CWL script which should merge the graphs files produced from the previous step. I need t=CWL to check the output directory and merge those graphs. My CWL script looks like following, . The input is an array of BAM files. 1. I need CWL command line tool to go check the existing ...
next-gen cwl rna-seq written 4 days ago by a.james120
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Did not find output file with glob pattern: for creating runtime output directory in CWL
... Dear All, I have a CWL script to run a python script. The commad line tool version of CWL is as following, cwlVersion: v1.0 class: CommandLineTool doc: Spladder baseCommand: [python, sladder.py] requirements: - class: InlineJavascriptRequirement - class: In ...
cwl written 22 days ago by a.james120
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Comment: C: How to calculate the sensitivity and specificity of set of expression dataset u
... Thank you sir, for detailed description. I would follow those steps. Yes these five were most significantly up-regualted within each subtype ...
written 5 weeks ago by a.james120
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Comment: C: How to calculate the sensitivity and specificity of set of expression dataset u
... Thanks for the reply. In my case I have no pheotype/metadata information other than defined 3 subtypes and the age group (adults or pediatric patients information). And I tried `lm()` model on the dataset, using top 5 Up-regulated genes from 3 subtypes to predict the `lm()` model. Then used `stepAIC ...
written 5 weeks ago by a.james120
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Comment: C: How to calculate the sensitivity and specificity of set of expression dataset u
... Thanks Kevin for the answer. The predictive model should be appiled on raw count or normlaized expression count? Also, in this case (RNA-seq) Bayseian predictive model would be a good choice? ...
written 5 weeks ago by a.james120
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How to calculate the sensitivity and specificity of set of expression dataset used in a validation cohort
... Hello All, I have a set gene which I used on a validation cohort, to find its ability to specifically classify cancer subtype, now I need to calculate the specificity and sensitivity of these genes for classifying the cancer subtypes. What would be the correct statistical approach/ tests to go for ...
gene rna-seq written 5 weeks ago by a.james120
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Comment: C: Error while parsing vcf file
... @Pierre Lindenbaum, apparently the issue is with vcf.reader parser doesn't suit for vcf 4.2 files. ...
written 18 months ago by a.james120
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Comment: C: Error while parsing vcf file
... No, I just highlighted it for bio-stars. There is no quote in real vcf file. ...
written 18 months ago by a.james120
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Comment: C: Error while parsing vcf file
... Here is the whole line which complaints, #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL 1 14748 . G C . alt_allele_in_normal;t_lod_fstar ECNT=1;HCNT=4;MAX_ED=.;MIN_ED=.;NLOD=29.34;TLOD=4.58;CSQ=C|non_coding_transcript_exon_variant|MODIFIER|WASH7P ...
written 18 months ago by a.james120
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Comment: C: Error while parsing vcf file
... Thats the first line of my vcf file I mean after header, and I am wondering 82, 2 is in int format isnt? ...
written 18 months ago by a.james120

Latest awards to a.james

Popular Question 8 months ago, created a question with more than 1,000 views. For GeneSCF gives out more pathways for genes compared to DAVID
Popular Question 8 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 8 months ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 11 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 16 months ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 17 months ago, created a question with more than 1,000 views. For How to find the frame shift information from fusion gene sequence
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq output from RNA-seq
Popular Question 23 months ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Student 2.2 years ago, asked a question with at least 3 up-votes. For ALL RNA-seq publicly available data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Scholar 2.3 years ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Pathway Graphs for gene set from RNA-seq
Popular Question 2.9 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 2.9 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data

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