User: Simon Anders

gravatar for Simon Anders
Simon Anders3.5k
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Location:
Zentrum für Molekularbiologie, Universität Heidelberg
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3 weeks ago
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9 years ago
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Posts by Simon Anders

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Job: applied methods development for single-cell sequencing
... At Heidelberg University, we have vacancies for 1 PhD student and 2 post-doc positions for computational scientists with skills in data science, statistics or bioinformatics. All three positions are related to projects applying single-cell sequencing techniques to questions of human biology, name ...
job computational biology single-cell written 21 days ago by Simon Anders3.5k
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Comment: C: p-values smaller than machine epsilon in DESeq2
... Or, to answer the second question very directly: Not at all. A very low p value means that either model asumption is wrong or the evidence against the null hypothesis with almost certainty. There is little point in seeing different levels between being almost certain. This is why I usually recomme ...
written 6 weeks ago by Simon Anders3.5k
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Comment: C: DESeq2 Time Series and "control" condition
... try results( dds, contrast = c( "Age", "M18", "M12" ) ...
written 8 weeks ago by Simon Anders3.5k • updated 8 weeks ago by Michael Love20k
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Job: PhD opportunity in Heidelberg for computational people
... We are looking for a talented and motivated PhD Student with computational expertise for a project on the use of single-cell transcriptomics on cancer samples at Heidelberg University / Heidelberg University Hospital / EMBL-MMPU. For more information, please see here. ...
job single-cell phd position written 8 weeks ago by Simon Anders3.5k
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Answer: A: latest version of R is 3.5.1 and it does not compatible with many Bioconductor p
... Do not use 'install.packages'. Instead, follow the installation instructions for Bioconductor: https://www.bioconductor.org/install/   ...
written 3 months ago by Simon Anders3.5k
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Comment: C: DESeq2 Multi factor, multi time point comparison design formula
... If you want to know whether your comparisons make sense, you need to tell us more about the biology of your experiment. What is a "scafffold" and what do you want to find out about it? ...
written 4 months ago by Simon Anders3.5k
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Answer: A: RNA-seq data analysis with two species using DESeq2
... If you find significant differences between the samples with behaviour 4 and behaviour 1, you cannot say whether this difference is due to the fact that the samples are from animals exhibiting different behavior or due to the fact that they are different species. Your observation that PCA shows most ...
written 4 months ago by Simon Anders3.5k
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Comment: C: RNA-seq data analysis with two species using DESeq2
... Why are you surprised that species explains the bulk of the variance? Also: Please always post the sample table with such questions and explain how the samples differ. ...
written 4 months ago by Simon Anders3.5k
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Answer: A: should I get the logarithm of count values when I use standard method
... No, of course not! Why would you think that? (Background: The DESeq manual states, as explicitly as possible and since the very first version, that the matrix should contain "read counts", i.e., integer numbers that count how many reads map to the gene. Nevertheless, I have been asked hundreds of t ...
written 6 months ago by Simon Anders3.5k
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Answer: A: ASE using DESeq2
... The estimateSizeFactor function does not use the design information. You will get the same size factors, no matter what design formula you specify. So, your code does not do what you think it does. I could try to explain now how to do it correctly, but I guess Mike's write-up does tha job, so I let ...
written 6 months ago by Simon Anders3.5k

Latest awards to Simon Anders

Guru 8 weeks ago, received more than 100 upvotes.
Popular Question 4 months ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: DESeq2: interaction term as in limma
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Popular Question 18 months ago, created a question with more than 1,000 views. For looping through a GRangesList object
Popular Question 18 months ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
Popular Question 18 months ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 2.0 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.7 years ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 2.7 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 2.7 years ago, created an answer that has been accepted. For A: DESEQ2 : When we merge technical replicates raw reads, do we need to divide by t
Scholar 2.7 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 2.7 years ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Student 2.9 years ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 3.2 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion

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