User: JoannaF

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JoannaF0
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Posts by JoannaF

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Comment: C: DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samp
... Thanks lot for your answer ! ...
written 18 months ago by JoannaF0
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DESEq2 Principal Component Analysis : generate two PCA, one with condition1 samples and an other with condition2
... Hi, I have 33 RNA-seq samples from two conditions which can be separated in other sub-conditions. I ran DESEq2 on all the dataset up to rld <- rlog(dds, blind=FALSE) Then, I would to run plotPCA into a subset of samples of each condition. Is this code right in order to do that ? For the fir ...
deseq2 pca written 18 months ago by JoannaF0 • updated 18 months ago by Michael Love26k
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Comment: C: DESeq2 : normalized counts
... Thanks a lot !! Joanna ...
written 18 months ago by JoannaF0
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DESeq2 : normalized counts
... Hi, I would to have a data frame with normalized counts of my RNA-seq data set. I used DESeq2 to analyse these data. This is the code I used to generate normalized counts : ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition) dds <- ...
rnaseq deseq2 normalized counts written 18 months ago by JoannaF0 • updated 18 months ago by Michael Love26k
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Answer: A: DESEq2 Principal Component Analysis with different genes biotypes (protein codin
... Thanks a lot for your answer ! It helps me a lot ! ...
written 19 months ago by JoannaF0
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DESEq2 Principal Component Analysis with different genes biotypes (protein coding, miRNAs, lncRNAs, etc)
... Hi, I would to generate different Principal Component Analysis using DESeq2, after rlog transformation. I would to generate one PCA for protein coding genes, one PCA for miRNAs, one PCA for lncRNAs, etc (for all gene_biotypes in my reference annotations). I have count files from 33 RNA-seq samples ...
deseq2 pca rlog transformation biotype written 19 months ago by JoannaF0
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Comment: C: CSAW : at which bam files are corresponding “up” regions
... Thanks for your quick answer ! Best regards, Joanna ...
written 3.7 years ago by JoannaF0
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Comment: C: CSAW: GAIN and LOSS of enrichment
... Thanks a lot for your answer ! The new post with my question and the R code is: "CSAW : at which bam files are corresponding “up” regions". Kind regards, Joanna ...
written 3.7 years ago by JoannaF0
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CSAW : at which bam files are corresponding “up” regions
... Hi, I have one question about gain and loss of enrichment with CSAW. Our bam files are: Our bam files are: bam.files <- c("sample1_rep1.bam", "sample1_rep2.bam", "sample2_rep1.bam") I would like to know at which files are corresponding “up” regions detected by CSAW : it is sample1 or sample2 ...
csaw up regions bam file gain and loss of enrichment written 3.7 years ago by JoannaF0 • updated 3.7 years ago by Aaron Lun25k
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Answer: A: CSAW: GAIN and LOSS of enrichment
... Hi, I have one question about gain and loss of enrichment with CSAW. Our bam files are: bam.files <- c("sample1_rep1.bam", "sample1_rep2.bam", "sample2_rep1.bam") I would like to know at which files are corresponding “up” regions detected by CSAW : it is sample1 or sample2 in this case ? Than ...
written 3.7 years ago by JoannaF0

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Popular Question 18 months ago, created a question with more than 1,000 views. For DESeq2 : normalized counts

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