User: Elucidata

gravatar for Elucidata
Elucidata120
Reputation:
120
Status:
Trusted
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Website:
https://elucidata.io/
Twitter:
elucidatacorp
Last seen:
1 day, 11 hours ago
Joined:
1 year ago
Email:
e**********@elucidata.io

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Posts by Elucidata

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Merge two vcf's, keep only intersection of REF/ALT alleles
... One of the common tools used to merge and intersect vcf files based on the REF/ALT alleles is bedtools intersect (also can be used as intersectbed). One can use this tool to find overlapping entries between files or exclusive entries between files by mentioning the corresponding flags of the tool. ...
written 12 days ago by Elucidata120
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Answer: A: Enrichment Score Interpretation
... **Gene Set Enrichment Analysis (GSEA)** is an analytical method to interpret gene expression data. ***Algorithm:*** - Consider a list (say L) in which genes are ordered according to some measure of correlation. The aim of GSEA is to decide if a gene set will in general happen towards the lower or ...
written 12 days ago by Elucidata120
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Answer: A: MOOC for AI and Machine learning for Bioinformatics
... Getting started with Bioinformatics is a long and exciting journey given that you are guided well in the right direction and are provided with excellent resources. For any beginner getting started with ML/AI in bioinformatics, would be to get a stronghold of Python and R for both of them provide po ...
written 20 days ago by Elucidata120
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Comment: C: Differential gene set analysis on TCGA data
... Hi, we do not intend to spam or break any other rules on Biostars. We respect all the forum rules. As a company we did not join to advertise our products, we just want to help our community. We just want to add our quick links as a signature, like other forums allow to do. ...
written 21 days ago by Elucidata120
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Comment: C: Scaled gene expression data and produced negative value
... Thanks for pointing it out. Have made the modifications. ...
written 4 weeks ago by Elucidata120
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Answer: A: Differential gene set analysis on TCGA data
... The [Xena Browser][1] provides an interactive framework to query TCGA datasets. You can select the TCGA-BRCA dataset in the Xena Browser and use PAM_50_mRNA_nature2012 annotation to classify samples into different subtypes, one of them is Basal-like. You can download the sample vs annotation mappi ...
written 4 weeks ago by Elucidata120
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Answer: A: How to analysis metabolomics data with pathway? Why library doesn't require my d
... In MetaboAnalyst, pathway analysis can be done in two ways: - You can provide a list of metabolites (KEGG IDs, HMDB IDs, or compound names). It does an over-representation analysis that tests whether compounds involved in a certain pathway is enriched compared by random hits. These metabolites cou ...
written 4 weeks ago by Elucidata120
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Answer: A: RNA seq analysis ( pre-processing)
... Following are some sources that shall help to get tumor along with control samples from TCGA: - [Xena Browser][1] is a consortium of processed TCGA, GDC, and other public cancer genomics data sources. It has a dataset with a combined cohort of GTEx, TCGA, and TARGET samples. 1. TCGA is a database ...
written 4 weeks ago by Elucidata120
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Answer: A: Scaled gene expression data and produced negative value
... OP mentioned in one of the comments that he is using rowScales functions for scaling and has not mentioned the package, while we guess it might be from [scrime][1] package. The reason for getting negative values is because rowScales scales the row in a way such that the values in each row would hav ...
written 4 weeks ago by Elucidata120
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Answer: A: Does GSVA normalize sampleset?
... GSVA is a method that is supposed to work on samples. - By subsetting, if you mean reducing the genes in the dataset then it will have an effect on the scores as the GSVA method fits a density function to each gene using all samples before using the cumulative density values from the distribution ...
written 4 weeks ago by Elucidata120

Latest awards to Elucidata

Appreciated 12 days ago, created a post with more than 5 votes. For A: Methylation data analysis
Autobiographer 21 days ago, has more than 80 characters in the information field of the user's profile.
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Methylation data analysis
Scholar 6 weeks ago, created an answer that has been accepted. For A: Methylation data analysis
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Methylation data analysis

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