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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 4.5 years ago by 52k • written 4.5 years ago by ▴ 70
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1.2k
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Any pointers on simulating cell outliers?
splatter simulation
7.0 years ago luke.zappia ▴ 50
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1.2k
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Could an experienced user of Polyester help me with some questions?
rna-seq polyester simulation time course
7.4 years ago fa.gholizadeh89 • 0
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1.9k
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How to simulate a count matrix using Polyester
simulation count matrix RNA-seq Polyester
updated 7.4 years ago by ▴ 210 • written 7.4 years ago by • 0
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1.3k
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Polyester - creating simulated reads based on raw count matrix
polyester rnaseq simulation
7.8 years ago sseo2 • 0
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1.4k
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Job: Post-doc in mathematical modeling on phenotypic evolution and embryonic development
job computational biology simulation evolution Gene network Job
7.8 years ago isaac.salazar • 0
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Job: postdoctoral position in Computational Biology/Statistics/Evolutionary Biology in Madrid, Spain
bioconductor R jobs C++ simulation Job
8.3 years ago Ramon Diaz-Uriarte ▴ 70
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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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