User: a.james
a.james • 120
- Reputation:
- 120
- Status:
- Trusted
- Location:
- Germany
- Last seen:
- 15 hours ago
- Joined:
- 4 years, 3 months ago
- Email:
- a******@dkfz-heidelberg.de
Posts by a.james
<prev
• 58 results •
page 1 of 6 •
next >
0
votes
0
answers
48
views
0
answers
... 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 ...
written 4 days ago by
a.james • 120
0
votes
0
answers
194
views
0
answers
... 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 ...
written 22 days ago by
a.james • 120
1
vote
1
answer
236
views
1
answers
... 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.james • 120
0
votes
1
answer
236
views
1
answers
... 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.james • 120
0
votes
1
answer
236
views
1
answers
... 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.james • 120
4
votes
1
answer
236
views
1
answer
... 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 ...
written 5 weeks ago by
a.james • 120
0
votes
0
answers
660
views
0
answers
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.james • 120
0
votes
0
answers
660
views
0
answers
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.james • 120
0
votes
0
answers
660
views
0
answers
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.james • 120
0
votes
0
answers
660
views
0
answers
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.james • 120
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1849 users visited in the last hour