User: debitboro

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debitboro70
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3 years, 10 months ago
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Posts by debitboro

<prev • 68 results • page 1 of 7 • next >
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Answer: A: Precision Medicine Bioinformatics: From raw genome and transcriptome data to cli
... Precision Medicine Bioinformatics: From raw genome and transcriptome data to clinical interpretation (PMBI01) 29 October 2018 - 2 November 2018 https://www.prinformatics.com/course/precision-medicine-bioinformatics-from-raw-genome-and-transcriptome-data-to-clinical-interpretation-pmbi01/ ...
written 5 days ago by debitboro70
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sortMeRNA before or after adapters trimming ?
... Hi Biostars community, Shall I use sortMeRNA before or after poly(A) tails removal and/or adapters trimming ? Thanks ...
rrna sortmerna rna-seq written 7 days ago by debitboro70
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Questions about STAR and Bowtie (not Bowtie2) mapping
... Hi all, I want to perform an alignment of short reads against a reference genome (human genome from Ensembl). For that I've used STAR, and Bowtie (not Bowtie2). I've some questions about that. 1- I've used STAR by setting the more important parameters as follows: --outFilterScoreMinOverLread ...
bowtie star uniquely mapped reads rna-seq written 10 days ago by debitboro70 • updated 10 days ago by Ram14k
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Comment: A: short RNA reads alignment
... Hi all, Thank you for your replies. Finally I've tried STAR and Bowtie (not Bowtie2). 1- I've used STAR by setting the more important parameters as follows: --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMatchNmin 15 Here is the final log file content gene ...
written 10 days ago by debitboro70
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short RNA reads alignment
... Hi biostars, I've short RNA reads (18-47 nt). I want to perform the alignment, for that I've two questions: 1- Can I use STAR to perform the alignment ? if no, what alignment program do you recommend me ? 2- Shall I align the reads against the reference genome (for example Homo_sapiens.GRCh38.dna. ...
alignment rna-seq short reads written 12 days ago by debitboro70
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Check variance stabilization transformation ?
... Hi all biostars, How can check if the variance stabilization transformation has worked well ? I've used the function getVarianceStabilizedData() of DESeq2 package as a VST method on RNASeq expression matrix, and now I want to check if the method has worked well or not ? Any idea ! Thanks in advan ...
deseq2 variance stabilization rna-seq written 4 weeks ago by debitboro70 • updated 4 weeks ago by swbarnes23.4k
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How can I get the OOB samples used for each tree in random forest model R?
... Is it possible to get the OOB samples used by random forest algorithm for each tree ? I'm using R language. I know that RandomForest algorithm uses almost 66% of the data (selected randomly) to grow up each tree, and 34 % of the data as OOB samples to measure the OOB error, but I don't know how to g ...
randomforest oob samples written 4 months ago by debitboro70
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How to calculate the AUC value for a ranger RF model ?
... Hi Biostars community, How can I calculate the AUC value for a ranger model ? Ranger is a fast implementation of randomForest algorithm in R. I'm using the following code to build the ranger model for classification purposes, and get the prediction from the model: #Build the model using ranger ...
auc value ranger randomforest classification written 8 months ago by debitboro70
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ggplot expression values as function of samples and classes
... Hi Biostars, Can anyone helps me on the following. I want to plot the expression values of miRNAs as function of samples using ggplot library. I've a dataframe "reduced_data" containing 50 samples and 3 miRNAs + one column "class" (class of each patient: 6 classes). reduced_data (ordered by class ...
ggplot classes mirna expression written 8 months ago by debitboro70 • updated 8 months ago by Ido Tamir4.8k
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Answer: A: Bug in RUV spike-in normalization?
... Hi student-t, I stated the same thing when I tried to run a reduced example. I don't know why Risso used the U matrix only ??? The corresponding code to what it has been stated in the article would be like: k <- min(k, max(which(svdWa$d > tolerance))) W <- svdWa$u %*% svdWa$d By ...
written 10 months ago by debitboro70

Latest awards to debitboro

Popular Question 3 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 3 months ago, created a question with more than 1,000 views. For RNA-Seq for DE analysis
Popular Question 3 months ago, created a question with more than 1,000 views. For Technical and Biological replicates
Popular Question 8 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 8 months ago, created a question with more than 1,000 views. For RNA-Seq for DE analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For RNA-Seq for DE analysis
Popular Question 13 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 13 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA

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