Man pages for RamsinghLab/arkas_staging
A package that complements Kallisto for quick, informative *seq analysis
| annotateFeatures | annotate rowRanges genes or transcripts against (say)... |
| calcTpm | given a vector or matrix of est_counts and the same for... |
| collapseBundles | Collapse bundles of transcripts, discard any that represent... |
| collapseByTss | groundwork for collapsing rows of a... |
| collapseTpm | Collapse bundles of transcripts, discard any with (default) <... |
| collapseTranscripts | Collapse transcripts, discarding any with low reads... |
| crossModels | Often times it is needed to cross compare edgeR results,... |
| dumpToBigWig | Dump the columns of a kexp to bigWig files. This requires... |
| ERCC_annotated | ERCC spike-in control annotations |
| extractIndexName | extract the transcriptome index used for a Kallisto hdf5 file |
| fastqFileUploadToBaseSpace | once the sraFastqHeaderToIlluminaStandard has been ran on SRA... |
| fetchAppSession | fetch app session variables from BaseSpace JSON |
| fetchKallisto | fetch one sample's worth of Kallisto estimates, perhaps with... |
| fitBundles | encapsulate limma/voom analysis for consistency with... |
| fitRepeats | repeat analysis is used for analysis of repeat regions from... |
| fitTranscripts | encapsulate limma/voom analysis and TMM normalization at... |
| geneWiseAnalysis | Downstream analysis of bundle-aggregated transcript abundance... |
| getKallistoVersion | get the running version of Kallisto in the default path (if... |
| indexKallisto | index transcriptome/transcriptomes |
| KallistoExperiment | Initializes a KallistoExperiment and performs some... |
| KallistoExperiment-class | A SummarizedExperiment subclass that stores multiple Kallisto... |
| KEtoSE | converts a kallistoExperiment object to SummarizedExperiment |
| mergeKallisto | Merge multiple Kallisto results, yielding a... |
| pairFastqFiles | figure out how a sample's runs can be properly paired (no SE... |
| parseFastqNames | like it says: parse the chunks of FASTQ file names to get... |
| remapSymbols | update transcript-/gene-level annotations for a... |
| repeatWiseAnalysis | Downstream analysis of bundle-aggregated repeat elements |
| rpkmToTpm | Converts RPKM or FPKM estimates to TPM. Per Colin Dewey, |
| runKallisto | run kallisto with fastq.gz files on a freshly generated or... |
| ruvNormalization | RUVSeq methods allow for proper normalization by using a GLM... |
| SEtoKE | convertes a summarizedExperiment to KallistoExperiment |
| showTnxBundles | Groups bundles of transcripts, discard any that represent... |
| sraFastqHeaderToIlluminaStandard | this script prepares fastq files downloaded from SRADb R... |
| transcriptWiseAnalysis | Analysis of raw transcript abundance estimates. |
| unannotatedTranscript | Structure for non annotated transcripts |
