Man pages for icetea
Integrating Cap Enrichment with Transcript Expression Analysis
| activeChrs | Match BAM headers bw files and get active chromosome list... |
| annotateTSS | Annotate the provided Transcription Start Sites |
| check_capSet | Check capset validity |
| demultiplexFASTQ | Demultiplex and tag fastq files using sample barcodes |
| detectDiffTSS | Detect differentially expressed Transcription Start Sites... |
| detectTSS | Detection of Trancription start sites based on local... |
| diffQCplots | Make DESeq2 or edgeR QC plots |
| exampleCSobject | Create example CapSet object |
| exportTSS | Export the detected TSS from CapSet object as .bed files |
| filterDuplicates | 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... |
| 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 |
| getMCparams | Get platform-specific multicore params |
| get_newfastq | Get data to create new ShortReadQ object after barcode... |
| getNormFactors | Calculate normalization factors from CapSet object |
| getranks | Assign feature ranks on a VariantAnnotation output |
| mapCaps | 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 |
| plotTSSprecision | Compare the precision of TSS detection between multiple... |
| 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 |
| splitBAM_byIndex | Split the composite BAM file using internal indexes (MAPCap) |
| splitBAM_byRepindex | Split the composite BAM file using replicate indexes (MAPCap... |
| split_fastq | Split paired-end fastq by barcodes |
| splitranks | Get features with the best rank for each TSS |
| strandBinCounts | Perform stranded Bin counts |
