activeChrs | Match BAM headers bw files and get active chromosome list (from restrict) (written by Aaron Lun, 12 Dec 2014, copied and modified here) |
annotateTSS | Annotate the provided Transcription Start Sites |
CapSet | Create a new CapSet object |
CapSet-class | Create a new CapSet object |
check_capSet | Check capset validity |
demultiplexFASTQ | Demultiplex and tag fastq files using sample barcodes |
demultiplexFASTQ-method | Demultiplex and tag fastq files using sample barcodes |
detectDiffTSS | Detect differentially expressed Transcription Start Sites between two conditions (test) |
detectDiffTSS-method | Detect differentially expressed Transcription Start Sites between two conditions (test) |
detectTSS | Detection of Trancription start sites based on local enrichment |
detectTSS-method | Detection of Trancription start sites based on local enrichment |
diffQCplots | Make DESeq2 or edgeR QC plots |
exampleCSobject | Create example CapSet object |
exportTSS | Export the detected TSS from CapSet object as .bed files |
exportTSS-method | Export the detected TSS from CapSet object as .bed files |
filterDuplicates | Filter PCR-duplicates from mapped files using internal UMIs |
filterDuplicates-method | Filter PCR-duplicates from mapped files using internal UMIs |
filterDups | Filter PCR-duplicates from BAM file using internal UMIs |
fitDiffTSS | Detect differentially expressed Transcription Start Sites between two conditions (fit model) |
fitDiffTSS-method | Detect differentially expressed Transcription Start Sites between two conditions (fit model) |
getBamFlags | Get flags to read from bam |
getChromBins | Get chromosome bins from BAM files |
getChromWindows | Get chromosome sliding windows from BAM files |
getGeneCounts | Get gene-level counts from TSS data |
getGeneCounts-method | Get gene-level counts from TSS data |
getMCparams | Get platform-specific multicore params |
getNormFactors | Calculate normalization factors from CapSet object |
getNormFactors-method | Calculate normalization factors from CapSet object |
getranks | Assign feature ranks on a VariantAnnotation output |
get_newfastq | Get data to create new ShortReadQ object after barcode trimming |
mapCaps | Map the data from 5' profiling techniques |
mapCaps-method | Map the data from 5' profiling techniques |
newCapSet | Create a new CapSet object |
numReadsInBed | Count the number of reads in a given GRanges |
plotPrecision | Plotprecision background script |
plotReadStats | Plot read statistics from the CapSet object |
plotReadStats-method | Plot read statistics from the CapSet object |
plotTSSprecision | Compare the precision of TSS detection between multiple samples |
plotTSSprecision-method | Compare the precision of TSS detection between multiple samples |
readsTo3p | preprocess reads to count only 3' overlaps |
readsTo5p | preprocess reads to count only 5' overlaps |
readsToCenter | preprocess reads to count only center overlaps |
sampleInfo | Retrieve and replace sample information of a CapSet object |
sampleInfo-method | Retrieve and replace sample information of a CapSet object |
sampleInfo<- | Retrieve and replace sample information of a CapSet object |
sampleInfo<--method | Retrieve and replace sample information of a CapSet object |
splitBAM_byIndex | Split the composite BAM file using internal indexes (MAPCap) |
splitBAM_byRepindex | Split the composite BAM file using replicate indexes (MAPCap data) |
splitranks | Get features with the best rank for each TSS |
split_fastq | Split paired-end fastq by barcodes |
strandBinCounts | Perform stranded Bin counts |