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downloads [2015/05/28 16:47] sotacam |
downloads [2015/06/02 15:03] sotacam [Differential expression on simulated data] |
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- | ====== Data used to test the tools included in R NOISeq package ====== | + | ====== Data used to test the R NOISeq package ====== |
===== ENCODE data ===== | ===== ENCODE data ===== | ||
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from Ensembl (release 68) using TopHat 1.4.1. Gene expression was quantified using the HTSeq Python package, | from Ensembl (release 68) using TopHat 1.4.1. Gene expression was quantified using the HTSeq Python package, | ||
version 0.5.3p3. | version 0.5.3p3. | ||
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+ | {{:prostatecancercountdata.txt.zip|Prostate Cancer count matrix}} | ||
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+ | ====== R code used to test the NOISeqBIO method ====== | ||
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+ | ===== Simulation algorithm ===== | ||
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+ | R scripts for simulating RNA-seq count data for two experimental conditions: | ||
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+ | {{:simulation_high.r|Simulation of HIGH variability scenarios}} | ||
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+ | {{:simulation_low.r|Simulation of LOW variability scenarios}} | ||
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+ | ===== Differential expression on simulated data ===== | ||
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+ | These scripts show how the differential expression methods were applied on simulated data sets: | ||
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+ | {{:methodsonsimulations.r|DE methods on simulations}} | ||
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+ | {{:globalsimulationsanalysis.r|Analysis of DE results}} | ||