Man pages for plger/RNAontheBENCH
RNAontheBENCH - Benchmark of RNAseq quantification and DEA
| analyzeSpikein | Comparison quantification with the expected spike-in... |
| auc | auc |
| benchmarkWrapper | A wrapper that performs the whole benchmark analysis |
| checkMatIntegrity | checkMatIntegrity |
| compareSimulated | Transcript-level benchmark of the simulated data |
| compareSpikeinDEcalls | compareSpikeinDEcalls |
| compareWithNanostring | Comparison with Nanostring |
| compareWithPCR | Gene-level comparison with RT-qPCR data |
| convertTx2Genes | Summarizes transcript quantifications to the gene level |
| counts2fpkm | Convert counts to FPKM values |
| counts2fpkmWrapper | Convert counts matrix to FPKM matrix |
| deNanostring | deNanostring |
| deNanostring.compare | deNanostring.compare |
| deSpikein | Runs a spike-in differential expression analysis. |
| deSpikein.compare | deSpikein.compare |
| donorm | normalizes a dataset |
| fc2mean | foldchange-to-the-mean |
| fcdev | Plots deviation from real foldchange by p-value |
| foldchange | foldchange |
| fpkm2tpm | Convert FPKM values to TPM values |
| getLinearNormalizers | getLinearNormalizers |
| getLogFC | Retrieves the log2(foldchange) |
| homomixes | Homogenizes the two spike-in mixes. |
| isCleanData | isCleanData |
| maketrans | Make transparent |
| MdAE | Median absolute error |
| mROC | mROC |
| myc | Plots sensitivity and specificity by p-value |
| package_sf_as_kal | Convert sailfish results for one or more samples to kallisto... |
| plColorMap | plColorMap |
| plGetModel | Retrieves a linear model, if possible. |
| plTryRead | plTryRead |
| posplot | Positives plot |
| pval2fc | Plots p-values according to real foldchange. |
| readBenchmarkResults | readBenchmarkResults |
| RNAontheBENCH-package | RNAontheBENCH - Benchmark of RNAseq quantification and DEA |
| ROC | ROC |
| runTests | Runs a differential expression analysis. |
| seqc.diff | seqc.diff |
| seqc.diff.example | seqc.diff.example |
| seqc.diff.plot | seqc.diff.plot |
| seqc.diff.sleuth | seqc.diff.sleuth |
| seqc.get.stats | seqc.get.stats |
| seqc.prepareData | seqc.prepareData |
| sf_to_hdf5 | Convert sailfish results for one sample to kallisto HDF5 |
| simStats | Writes a table of metrics comparing two vectors |
| sleuth_prep_sailfish | sleuth_prep_sailfish |
| sleuthWrapper | Runs a spike-in differential expression analysis using... |
| zscore | z-score |
