User: Assa Yeroslaviz

gravatar for Assa Yeroslaviz
Assa Yeroslaviz1.3k
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Munich, Germany
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Posts by Assa Yeroslaviz

<prev • 265 results • page 2 of 27 • next >
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Comment: C: Error in tximport, unused argument (reader = read_tsv)
... did you try it without the parameter? ...
written 7 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
... is your count data stored in exp or ecp?   ...
written 7 weeks ago by Assa Yeroslaviz1.3k
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Answer: A: RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
... that is correct. try str(dds ) from the example and than also str(mydds) from your data and see if they have the same strucutre.   but to make your life easier Michael Love already created a package to import Kallisto data into DESeq2. take a look here ...
written 7 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: converting a GRangesList object with different lengths into a data frame
... Thanks for  the suggestion of this function. It is worth knowing for later cases. I know about the problem of exon, luckily we are working on S. cerevisiae and have no introns problem, as we are interested in the complete transcript. But this function looks very interesting. ...
written 9 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: converting a GRangesList object with different lengths into a data frame
... Thanks Michael, this is really smooth. I know this is a weird presentation of the data. I need this big data.frame of scores to be able to plot (either as a heat-map or lines plot) the gene intensities on top of each other. For that reason I needed the "gene lengths" to be identical. On my X-axis I ...
written 9 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: converting a GRangesList object with different lengths into a data frame
... Thanks Marcel for the suggestion of RaggedExperiment, But this is not what i needed, as I already know, that there are no common regions. This is not what I am looking for here. The first option I have already thought of. In my case I have over 3000 genomic regions, many of them have an identical le ...
written 9 weeks ago by Assa Yeroslaviz1.3k
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converting a GRangesList object with different lengths into a data frame
... Following my workflow and advancing one stye at a time, I would now like to convert a GRangesList object into a data.frame, where each of the score columns (meta data columns) of the different GRanges in the list are seaprate columns in the data frame such as : >tiles.list GRangesList object of ...
genomicranges grangeslist dataframe irangeslist lists written 9 weeks ago by Assa Yeroslaviz1.3k • updated 9 weeks ago by Michael Lawrence9.8k
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Comment: C: summarize scores of GRanges into bins
... +1 more. This is amazing, how you can fit anything in R. Thanks a lot for the explanation.  ...
written 10 weeks ago by Assa Yeroslaviz1.3k
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summarize scores of GRanges into bins
... As a third part of my GenomicRanges analysis, I would to further manipulate my GRangesList object. I have created a GRangesList objaect after subsetting my intensities to only the regions of the genes in the gtf file. This gave me a GRangesList object looks like that: GRangesList object of length ...
genomicranges grangeslist findoverlaps bin written 10 weeks ago by Assa Yeroslaviz1.3k • updated 10 weeks ago by Michael Lawrence9.8k
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Comment: C: subsetByOverlaps with Multimapping
... thanks a lot. I thought there might be a better way to do it. ...
written 10 weeks ago by Assa Yeroslaviz1.3k

Latest awards to Assa Yeroslaviz

Appreciated 7 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Popular Question 7 months ago, created a question with more than 1,000 views. For extract intensity values from AffyBatch
Popular Question 9 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
Popular Question 19 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
Appreciated 19 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Supporter 20 months ago, voted at least 25 times.
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Problem with biomart's listMarts function
Popular Question 2.1 years ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Scholar 2.4 years ago, created an answer that has been accepted. For A: could not find symbol "keepNA" in environment of the generic function
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