User: Nitin Sharma

gravatar for Nitin Sharma
Nitin Sharma30
Reputation:
30
Status:
New User
Location:
Institute for Cancer Research, Dept. of Tumor Biology, Oslo University Hospital, Oslo, Norway
Twitter:
CuriusScientist
Scholar ID:
Google Scholar Page
Last seen:
4 days, 15 hours ago
Joined:
4 years, 3 months ago
Email:
e****************@gmail.com

Posts by Nitin Sharma

<prev • 14 results • page 1 of 2 • next >
0
votes
0
answers
65
views
0
answers
Low-coverage whole-genome sequencing (LC-WGS) or ultra low-pass WGS analysis
... I am new to the genome analysis and want to analyse ultra low-pass WGS data for copy number variation analysis. It will be really helpful if the members of the community can check if the approach I have taken is correct # fetch information for read groups header=$(zcat ${sample_name}_R1_00 ...
genome lc-wgs next-gen sequencing ichorcna written 12 days ago by Nitin Sharma30
0
votes
2
answers
4.9k
views
2
answers
Answer: A: Finding Variable Genes in Seurat, scRNA-seq
... > I found that changing x.low.cutoff between 0.0125 (in the PBMC 3k tutorial) and 0.1, for example, will have a huge effect on the number of variable genes > **@igor,** this is bound to happen as the number of genes is higher below 0 ( as can be seen by the dense plotting) I was facing the ...
written 9 months ago by Nitin Sharma30
0
votes
0
answers
711
views
0
answers
cBioPortal genetic profile id and mutational data analysis
... Dear all, I recently started using cBioPortal and struggling to understand the terminologies used and what is the importance and application of a particular one over another and apologies for a long and naive question. The aim of my study is to understand the mutational profile. for the cancer st ...
gistic cna tcga cbioportal mutation assessor written 19 months ago by Nitin Sharma30
0
votes
0
answers
1.1k
views
0
answers
Comment: A: how to find a particular GEO dataset or cohort in cBioportal and TCGA
... Many thanks to @igor for clarifying my doubts :) **how you think can I proceed with the following task** 1. I need to find the mutations in public databases 2. compare with in-house experimental results 3. perform analysis **Can I use the data/results from cBioPortal with those not part of cB ...
written 20 months ago by Nitin Sharma30
0
votes
0
answers
1.1k
views
0
answers
Comment: C: how to find a particular GEO dataset or cohort in cBioportal and TCGA
... That clears some of my doubts ...
written 20 months ago by Nitin Sharma30
0
votes
0
answers
1.1k
views
0
answers
Comment: C: how to find a particular GEO dataset or cohort in cBioportal and TCGA
... I can see that in the link mentioned by you cohort: GDC TCGA Prostate Cancer (PRAD) (11 datasets) and cohort: TCGA Prostate Cancer (PRAD) (22 datasets) what I want to know is how can I find what datasets are part of those 11 and 22 datasets? If I am not wrong some of them, if not all, must be par ...
written 20 months ago by Nitin Sharma30
0
votes
0
answers
1.1k
views
0
answers
how to find a particular GEO dataset or cohort in cBioportal and TCGA
... I am very new to the field of Cancer genomics so this might be very naive query I am interested in finding the dataset of the following study "Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples" the data is submitted to GEO (Accession Number: **GSE17599**). ...
geo R gdac tcga cbioportal written 20 months ago by Nitin Sharma30
1
vote
0
answers
542
views
0
answers
what is difference between preliminary somatic mutations, somatic mutations and validated somatic mutations
... Dear All, I recently started working in Cancer Genomics and started to work on cBioPortal. As I was scrolling through the FAQs of cBioPortal I came across this information "Why do some cancer studies have mutation data and others do not? We store mutation data for published cancer studies. We do n ...
tcga somatic mutations cbioportal written 20 months ago by Nitin Sharma30
3
votes
1
answer
869
views
1
answer
Confusion in Tophat2 input files
... dear all, This might be very silly question but i hope you can help to clear my doubts from TopHat mannual tophat [options]* [reads1_2,...readsN_2] Now, if i have a control and treated biological triplicate samples as paired-end reads what will be the right command 1) tophat [options]* cont ...
tophat alignment rna-seq written 3.0 years ago by Nitin Sharma30 • updated 3.0 years ago by WouterDeCoster41k
0
votes
1
answer
4.3k
views
1
answers
Comment: C: DESeq2 model design: dose and time effect
... thanks for the reply.  now things are getting more clear.  I can certainly collaborate with a statistician but I need to understand things myself.   will read  "Statistical Models" by Freedman mentioned by you in order to get improve my stats. thanks for all the help. ...
written 4.2 years ago by Nitin Sharma30

Latest awards to Nitin Sharma

Popular Question 8 weeks ago, created a question with more than 1,000 views. For DESeq2 model design: dose and time effect
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeq2 model design: dose and time effect

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1268 users visited in the last hour