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Questions related from Snijesh V.P.
I have thousands of samples from `TCGA` retrieved using `TCGABiolinks`. I want to remove the `batch effect` from the datasets. It's mentioned that batch can be detected from sample ID itself How...
09 March 2023 3,544 0 View
which platform is better for performing microarray data analysis? agilent, affymetrix or illumina
10 April 2021 3,953 3 View
Tumor mutational burden (TMB) is a measure of the number of gene mutations inside the cancer cells. TMB of a tumor sample is calculated by the number of non-synonymous somatic mutations per...
02 September 2020 4,877 1 View
Is there any database or tool where I can retrieve list of proteins detectable by immune histochemistry (IHC)?
03 August 2020 7,897 2 View
what is the longest deletion or insertion that can be detected in next generation sequencing data analysis
27 February 2020 3,168 3 View
I have analyzed the dataset of GSE38132 from gene expression omnibus. The data is from cell line breast cancer ZR-75-1 which comprises of 9 conditions with 4 replicates for each condition making...
17 February 2020 6,006 4 View
I have 4 sample [control, pre-treatment, post-treatment, metastais] with 4 replicates which make total 4x4 = 16 samples I want to perform comparison of control with all other groups. For the said...
13 February 2020 6,584 2 View
I have two batches of samples which were collected during two time period. If I perform batch correction to remove batch effect will it affect the downstream analysis of gene expression studies?
20 December 2019 1,052 3 View
MedDRA is a clinically-validated international medical terminology used by regulatory authorities and the regulated biopharmaceutical industry. It contains about 1440 Lowest Level Terms (LLTs)?...
22 February 2019 2,831 0 View
I want to extract the data from the internet with specific medical terms. Which are the available tools with best accuracy or output?
07 February 2018 6,940 5 View
Hi, I think there are about 80 organs in the human body. When I searched for list of all organs different sites are showing different list. Are there any books or publication that clearly mentions...
11 November 2017 9,039 4 View
In exome sequencing, specific interval list (-L) is used by each company to capture particular region. But all exome in the genome will be in particular regions (the default region of exomes...
10 October 2017 988 4 View
Consider a gene, OPN, in four individuals, which has mutation in a particular location of the gene. What is the chance of the individuals getting four different diseases?
13 September 2017 3,140 13 View
There are various genes reported for as somatic variants (not germline) in breast cancer. So is it possible for clinician or doctor to say or confirm whether the individual is affected with breast...
26 July 2017 2,083 3 View
I want to detect the somatic mutations for breast cancer disease. Can anyone tell me about the major differences in detecting somatic mutations from blood sample and tissue samples
21 July 2017 10,150 3 View
Breast cancers are classified into different types and sub-types. Are there any methods available to classify breast cancer based on mutations in the gene?
21 July 2017 6,256 10 View
May be a general question; sometimes stupidity too.... For example, cancer is caused by somatic mutation in the genome. And treatment has been given to the patient. So what is the chance of change...
18 July 2017 7,787 4 View
I know it is possible to identify germline mutations from the blood sample. But, I have serious doubt regarding detecting somatic mutations from the blood sample. Generally, somatic mutations are...
12 July 2017 8,114 9 View
Which all tools or packages would you recommend to me for clinical NGS data analysis. The aim is, at the end, I need the output with the best accuracy Tools or packages which I have...
07 July 2017 7,592 7 View
For clinical significance, what are the parameters should I consider for sequencing a sample. For example terms like High read depth
04 July 2017 4,131 1 View
Presently, there are many methods to calculate functional similarity (semantic similarity) between the genes. But there are three domains associated with any gene i.e., Molecular Function (MF),...
17 May 2017 4,242 2 View
I want to know, are there any companies or hospitals in India that offers genetic test for cancer, especially breast cancer
11 May 2017 1,741 3 View
I want to perform most accurate variant calling by implementing a perfect pipeline. I want to predict both somatic and germline mutations Please tell me your suggestions.
14 March 2017 511 11 View
I want to align my reads to reference genome. To date several tools are avilable like BWA, bowtie2 etc. Which tool is more accurate, sensitive and rapid for the said purpose? Thanks
06 March 2017 1,111 7 View
I am expecting most reliable and frequently mutated genes for Breast Cancer in Indian Population. Is text mining the only option?
02 March 2017 5,214 1 View
Presently, I am working on breast cancer. I want to know collecting which type of sample is better to understand the disease pathogenesis. 1. Blood Sample 2. Tissue Sample
20 February 2017 4,410 3 View
My plan is to develop a tool that predicts mutations in user input genome. I have collected some set of genes and their corresponding sequence. The nucleotide sequence positions of genes are...
13 February 2017 9,154 2 View
In genome data, gene is specified as TP53 with chromosome location (chr17:7565097-7590856). But when I serached this region in NCBI-Nucleotide,...
06 February 2017 5,517 4 View
I have set of genes with their nucleotide sequence (includes exons, introns everything) and I want to extract only coding region from these sequence. 1. How can I do it? 2. Is there any online...
04 February 2017 6,139 3 View
Recently, I came to know about a mobile DNA sequencer launched by Oxford (MinION). 1. What about Its efficiency and the reagents required for sequencing? 2. What are data anlysis tools used, once...
30 January 2017 974 2 View
I have just started my research on breast cancer based on mutational studies. In what all way a nanopore sequencing device can help me to drive research in heights. Here I have attached two links...
17 January 2017 9,235 0 View
I am in a research to identify key signatures involved in breast cancer in Indian population. I want to know, is there any database available related to breast cancer in India. I know about The...
02 January 2017 2,753 5 View
Using FastQC, I have checked the over all quality of the file. The output file contains much count of over represented sequences. I simply performed blast on these sequences, and surprisingly they...
29 December 2016 4,345 6 View
I want to know what all combination of drugs are applied to treat rheumatoid arthritis? For example, combination methotrexate and sulfasalazine are given to treat RA.
02 May 2014 145 6 View
I want to know what percent of total population is affected with RA? If possible provide me the details through graphs, pie charts, or any statistical measures?
21 April 2014 9,530 1 View
Basic steps in GENESPRING
26 November 2013 9,316 0 View
Docking with Schrodinger.
10 November 2013 2,203 0 View
Novel target proteins for rheumatoid arthritis.
24 October 2013 5,283 1 View
Rheumatoid Arthritis
10 October 2013 7,206 4 View
