Man pages for mffrank/RNAseqToCustomFASTA
Produce Custom Protein Fasta Databases from RNAseq Data
| concatenateFastas | Concatenate all fastas in a Folder. |
| downloadAnnotations | Download transcriptome annotatin from Ensemblin a format that... |
| filterDetectedTranscripts | Filter FPKM Table |
| filterSpacePlot | Generate a Junction Summary Report |
| finishFasta | Finish a raw fasta file for analysis |
| FPKMhist | Output Histogram of FPKM values |
| FPKMhistProteincoding | Output Histogram of FPKM values for protein-coding vs. non... |
| FPKMsummaryReport | Print Pdf with plots to help evaluate FPKM distribution |
| getAltSpliceProteins | Get alternatively spliced proteins |
| getBioMart | Download uniprot ids from BioMart |
| getCufflinksFPKM | Import FPKM from Cufflinks |
| getCufflinksgeneFPKM | Takes Cufflinks genes.fpkm_tracking output files as input and... |
| getCufflinksgtfFPKM | Takes Cufflinks gtf output files as input and outputs a named... |
| getCufflinkstranscriptFPKM | Takes Cufflinks isoforms.fpkm_tracking output files as input... |
| getProteinCoding | Convert FPKM Table with transcript ids to protein ids |
| getSNVandINDEL | Annotate Variants |
| getStarJunctions | Read in STAR junctions |
| getVcfs | Read Vcf files to GRanges |
| junctionSummaryReport | Plot the distribution of your splice junction types |
| makeDict | internal, makes named vector dict |
| OutputJunctions | Output Splice Junction FASTA |
| OutputNovelJun | Generate peptide FASTA file that contains novel junctions. |
| plotJuncReplicateOverlap | #' Generate a Junction Summary Report #' @details Saves a... |
| plotSDvsMeanExpression | Scatterplot of sd vs log transformed expression |
| plotSNVReplicateOverlap | Plot the overlap of identified Variants between replicates |
| VariantSummaryReport | Generate a Variant Summary Report |
