User: nicolas.hipp

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Posts by nicolas.hipp

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Masigpro and negative binomial regression
... I have a time course RNAseq data from 8 time-points with 3 replicates per sample. These data were aligned with STAR, I get the featureCount output. With these file, I wan't to use MasigPro package to evaluate which genes are moving during this process. But I've got a problem with the notion of negat ...
R rna-seq written 2.9 years ago by nicolas.hipp0 • updated 2.8 years ago by Biostar ♦♦ 20
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Comment: C: Differences between Cufflinks results and home-made FPKM values
... Ok thanks for the help ;) ...
written 2.9 years ago by nicolas.hipp0
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Comment: C: Differences between Cufflinks results and home-made FPKM values
... Oh yes, thanks for this explanation, I forgot the multi mapperparameters... sorry for the naive question .. I still try to understand the calcul of the length, when I extract information from BACH2 gene for eg, I found that the gtf file contains the length of each exon, utr, gene length and "transc ...
written 2.9 years ago by nicolas.hipp0
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Differences between Cufflinks results and home-made FPKM values
... Hi everyone, I have a problem to understand how Cufflinks calculate FPKM : There are a lots of posts on this issue, I read that FPKM= Number of mapped fragments / (length of the gene /1000) / (size of the libraries / 10^6) I have output from featureCount which give me raw counts and the length o ...
rna-seq written 2.9 years ago by nicolas.hipp0 • updated 2.9 years ago by Devon Ryan97k
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Comment: C: Time course analysis of RNAseq data
... Hi, Thanks for these very informative informations, It's seem to really fit with my question ;) ...
written 2.9 years ago by nicolas.hipp0
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Time course analysis of RNAseq data
... Hello everyone, I have a time course dataset from RNAsequencing. Tipically it's bulk RNAseq, with 8 time-points and 3 replicates per sample. I was wondering if there is something like the "pseudo-time" from monocle package (single cell RNAseq) to order my sample on one dimension? In the PCA genera ...
rna-seq written 2.9 years ago by nicolas.hipp0 • updated 2.9 years ago by Jean-Karim Heriche24k
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Answer: A: Spike-in RNA in single cell experiment
... Support sent me the sequences. sorry for this useless post ;) ...
written 3.1 years ago by nicolas.hipp0
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Spike-in RNA in single cell experiment
... Hello everyone, I look to setup a single cell-RNAseq experiment with the C1 fluidigm platform. In the [protocol][1], the advice to use Spike-in RNA for normalization ([Ambion AM1780][2]). So I look on the website of thermofisher, but I cannot find any sequences of these Spike-in. I made some resear ...
rna-seq written 3.1 years ago by nicolas.hipp0
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Comment: A: Strand Specificity in dUTP protocol
... Thanks a lot for this quick answer :) It's perfect :) ...
written 3.5 years ago by nicolas.hipp0
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Strand Specificity in dUTP protocol
... Hi everyone, I'm a beginner in RNAsequencing analysis, so I apologize for naive questions :) I have single end RNAseq datas from human prepared by NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina. I used STAR for alignments and now I would like to summary readCount using FeatureC ...
rna-seq written 3.5 years ago by nicolas.hipp0

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Generate Heatmap after DEseq2 analysis

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