User: Paul

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Paul750
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Posts by Paul

<prev • 49 results • page 1 of 5 • next >
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Finding overrepresented sequence motifs in a set of transcripts
... Hello, I have a list of miRNAs that I belive to be co-regulated post-transcriptionally. I would like to query the sequence of the mature miRNAs for over-represented sequence motifs. Does anybody have any idea if there is an exsiting tool that could be easily adapted to solve this problem? Thanks! ...
sequence mirna written 4.8 years ago by Paul750 • updated 4.8 years ago by pld4.8k
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Paper(S) Discussing Issues In Quality Assessment Of Ngs Data
... Hi, I'm wondering if anyone is aware of any good review papers outlining the main issues in quality assessment of NGS data, particularly Illumina RNA-seq data if at all possible. I've used FastQC for quality assessment, but it isn't published and I'm wondering if there are other papers which back ...
quality next-gen rna sequencing written 7.2 years ago by Paul750 • updated 7.2 years ago by Ian5.4k
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Comment: C: Generate All Possible Permutations Of Sample Labels In R
... Fair point, for reasons very specific to this microarray platform and the analysis we're doing I need to run these permutations through limma though! Thanks for the suggestion though! ...
written 7.2 years ago by Paul750
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Comment: C: Generate All Possible Permutations Of Sample Labels In R
... Yep Obi, you got that right, see "Chris Millers" message for how to produce it. Startlingly straightforward once you know how! ...
written 7.2 years ago by Paul750
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Comment: C: Generate All Possible Permutations Of Sample Labels In R
... combn(labels, 5) from the labels vector in my original post is exactly what I'm looking for. ...
written 7.2 years ago by Paul750
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Comment: C: Generate All Possible Permutations Of Sample Labels In R
... Yes! This produces exactly what I was looking for: a <- c(1,2,3,4,5,6,7,8,9,10) combn(a, 5) Produces a matrix with 252 columns. Now All I need to do is remove the duplicates and I've got the 126 I was looking for! ...
written 7.2 years ago by Paul750
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Generate All Possible Permutations Of Sample Labels In R
... Hi, I'm trying do some permutation testing on microarray data in R and the sample labels look like this: labels <- c("case_1", "case_2", "case_3", "case_4", "case_5", "control_1", "control_2", "control_3", "control_4", "control_5") To permute them I realize I could just repeatedly ...
R microarray written 7.2 years ago by Paul750 • updated 7.2 years ago by Obi Griffith17k
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Quantiles Normalization On Massive Dataset
... Hi, I've got a massive dataset of 160 Affy Exon arrays that I need to quantiles normalize at probe level (the reasons for which are complicated!), which means ~6 million probes per sample. Trying to load the into memory maxes out 32gigs of memory on one of our cluster nodes. I clearly need to fin ...
normalization written 7.3 years ago by Paul750 • updated 5.4 years ago by Biostar ♦♦ 20
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Datasets For Which There Is Microarray And Rna-Seq Data On The Same Samples
... Hi, I'm wondering if anyone is aware of datasets for which there is publicly available microarray and RNA-seq data on the same samples? So far I've come up with the HapMap CEU and YRI samples: http://www.nature.com/nature/journal/v464/n7289/abs/nature08903.html http://www.nature.com/nature/journa ...
rna microarray written 7.4 years ago by Paul750 • updated 7.4 years ago by Obi Griffith17k
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Comment: C: Using Fasta Sequence Reads In Galaxy
... There data is from this paper "http://www.biomedcentral.com/1471-2164/10/161" and is available here "http://www.picb.ac.cn/Comparative/data.html". Unfortunately the data is only available in fasta format. I'd like to use Bowtie (or any other suitable aligner) map the data and cufflinks (or some suit ...
written 7.5 years ago by Paul750

Latest awards to Paul

Supporter 7.1 years ago, voted at least 25 times.
Student 7.2 years ago, asked a question with at least 3 up-votes. For Paper(S) Discussing Issues In Quality Assessment Of Ngs Data
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Datasets For Which There Is Microarray And Rna-Seq Data On The Same Samples
Good Question 7.4 years ago, asked a question that was upvoted at least 5 times. For Datasets For Which There Is Microarray And Rna-Seq Data On The Same Samples
Student 7.4 years ago, asked a question with at least 3 up-votes. For Datasets For Which There Is Microarray And Rna-Seq Data On The Same Samples
Appreciated 7.8 years ago, created a post with more than 5 votes. For Tool For Quickly Establishing If Two Genes May Be Co-Regulated
Student 7.8 years ago, asked a question with at least 3 up-votes. For Tool For Quickly Establishing If Two Genes May Be Co-Regulated
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Good Question 7.8 years ago, asked a question that was upvoted at least 5 times. For Tool For Quickly Establishing If Two Genes May Be Co-Regulated
Popular Question 7.8 years ago, created a question with more than 1,000 views. For R Data.Frame To Latex Table With Formatting Of Decimal Points
Student 7.8 years ago, asked a question with at least 3 up-votes. For R Data.Frame To Latex Table With Formatting Of Decimal Points
Student 7.9 years ago, asked a question with at least 3 up-votes. For Possible Reasons For Intronic Snp Coming Out Top Of Gwas.
Popular Question 7.9 years ago, created a question with more than 1,000 views. For Possible Reasons For Intronic Snp Coming Out Top Of Gwas.
Popular Question 7.9 years ago, created a question with more than 1,000 views. For Possible Reasons For Intronic Snp Coming Out Top Of Gwas.
Teacher 7.9 years ago, created an answer with at least 3 up-votes. For A: Microarrays And Gene Regulation
Student 7.9 years ago, asked a question with at least 3 up-votes. For Why So Many Missing Genotypes In 1000 Genomes Data?
Popular Question 8.2 years ago, created a question with more than 1,000 views. For Best Mirna Target Prediction Algorithms
Popular Question 8.2 years ago, created a question with more than 1,000 views. For Best Mirna Target Prediction Algorithms
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Student 8.2 years ago, asked a question with at least 3 up-votes. For Best Mirna Target Prediction Algorithms
Student 8.2 years ago, asked a question with at least 3 up-votes. For Tool For Eqtl Mapping
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Popular Question 8.4 years ago, created a question with more than 1,000 views. For Easy Way To Get 3' Utr Lengths Of A List Of Genes
Student 8.4 years ago, asked a question with at least 3 up-votes. For Easy Way To Get 3' Utr Lengths Of A List Of Genes

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