User: The

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The90
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90
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Posts by The

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Comment: A: MSA of very long sequences?
... However given the length of sequences I guess it would be too much for most existing tools unless they are run on a high capacity computer cluster ...
written 8 months ago by The90
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Answer: A: MSA of very long sequences?
... "Muscle" mentions the following: "2.3 Large alignments If you have a large number of sequences (a few thousand), or they are very long, then the default settings of may be too slow for practical use. A good compromise between speed and accuracy is to run just the first two iterations of the algorit ...
written 8 months ago by The90
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Comment: C: Fetching Ribosomal protein sequences of Saccharomyces cerevisiae and E. Coli
... Thanks. This method works for my purpose ...
written 11 months ago by The90
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Fetching Ribosomal protein sequences of Saccharomyces cerevisiae and E. Coli
... Hello All, Can anybody suggest some way to get all the Ribosomal proteins from S. cerevisiae an E. coli, preferably in the UniProt format. Thanks ...
ribosomal protein sequence written 11 months ago by The90
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Answer: A: Future direction of Gene Set Enrichment Analysis
... One important point is correlation between gene expression so independence assumption doesn't hold true. Some methods addressed this issue https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458527/ ...
written 14 months ago by The90
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Comparing time series expression data
... Hello I wish to know if you can suggest any articles /methods/software which are used for comparing two time series gene expression studies. One of the software STEM can compare gene clusters (of similar profiles) with clusters from the 2nd study. It calculates correlation between clusters and the ...
time series gene expression written 14 months ago by The90 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Mapping multiple expression data on KEGG genes and metabolites
... I tried Paintomics today with some of the example files: it appears to work correctly. However, I didn't try with any of my own files. Alternatively, you can have a look at "Vanted" which seems to have some very nice features. https://link.springer.com/article/10.1186/1471-2105-7-109 https://im ...
written 14 months ago by The90
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Normalization of log-fold-change ratios when there is a global shift in expression
... Hello All, Usually, for test vs control studies of comparative gene or protein expression studies we assume that the there is NO major differences in global gene expression between the control and the case. Accordingly for log expression ratios of case/control is often median or mean shifted so as ...
expression fold-change written 20 months ago by The90 • updated 20 months ago by Carlo Yague4.3k
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Feature(Gene) selection using R Caret package: Error in seeds[[num_rs + 1L]] : subscript out of bounds
... Hello All, I've a dataset of six samples and 1530 genes(features) and wish to know the the importance of features. I'm trying to use the "Rank Features By Importance" as mentioned in [Feature Selection with the Caret R Package][1]. I'm using the following code: rm(list=ls()) set.seed(1234 ...
feature-selection R machine-learning biomarker written 22 months ago by The90
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User defined gene or metabolite set in globaltest
... Hello all, I'm a new user of the Globaltest method. Is it possible to input user defined gene or metabolite set for the globaltest algorithm in Bioiconductor or any other implementations? Thanks in advance ...
enrichment globaltest gene set written 22 months ago by The90

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Popular Question 6 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Epic Question 7 months ago, created a question with more than 10,000 views. For R: Scaling the rows of a matrix
Popular Question 8 months ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 8 months ago, created a question with more than 1,000 views. For Distance between two gene sets
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Great Question 22 months ago, created a question with more than 5,000 views. For R: Scaling the rows of a matrix
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Distance between two gene sets
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Fisher'S Exact Test For Gene Rank Enrichment
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Using Perl Text::Wrap For Wrapping Text
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Fisher'S Exact Test For Gene Rank Enrichment
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Scholar 3.6 years ago, created an answer that has been accepted. For A: Mapping multiple expression data on KEGG genes and metabolites

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