Man pages for wzthu/ATACFlow
An Easy-to-use Systematic pipeline for ATACseq data analysis
| AddMissingCells | AddMissingCells |
| ApplyMatrixByGroup | Apply function to integration sites per base per group |
| AssignFragCellnames | AssignFragCellnames |
| atacPipe2 | Pipeline for single replicate case-control paired-end... |
| ATACProc-class | Base class of this package |
| atacRepsPipe | Pipeline for multi-replicates case paired-end sequencing data |
| atacRepsPipe2 | Pipeline for multi-replicates case-control paired-end... |
| BamToBed | Convert bam format to bed format. |
| BedToBigWig | generate BigWig file from BED file |
| BedUtils | process bed file with limit memory |
| BinarizeCounts | Binarize counts |
| Bowtie2Mapping | Use bowtie2 aligner to map reads to reference genome |
| Cells-set | Set and get cell barcode information for a Fragment object |
| Cells-set-.Fragment | Cells |
| ChunkGRanges | ChunkGRanges |
| CollapseToLongestTranscript | CollapseToLongestTranscript |
| CountFragments | Count fragments |
| CreateFragmentObject | Create a Fragment object |
| CutSiteCountR | Count cut site number in given motif region and plot... |
| CutSitePre | Extract ATAC-seq cutting site from bed file. |
| dot-f_dowle2 | replace NA to 0 |
| dot-write10xCounts | Write count data in the 10x format |
| esATAC-package | An Easy-to-use Systematic pipeline for ATACseq data analysis |
| Extend | Extend |
| ExtractCell | ExtractCell |
| ExtractFragments | ExtractFragments |
| FastQC | Quality control for ATAC-seq data. |
| FeatureMatrix | Construct a feature x cell matrix from a genomic fragments... |
| FilterCells | Filter cells from fragment file |
| FindAdapter | Use AdapterRemoval to identify adapters |
| fragCreate | Create Fragment object |
| FragInRegions | FragInRegions |
| FragLenDistr | Quality control for fragment length distribution |
| Fragment-class | The Fragment class |
| Fragments | Get the Fragment objects |
| Fragments-set | Fragments |
| FRiPQC | Quality control for fraction of reads in peaks (FRiP) |
| GetCellsInRegion | GetCellsInRegion |
| GetFragmentData | Get Fragment object data |
| GetGRangesFromEnsDb | GetGRangesFromEnsDb |
| getMotifInfo | Generate PFMatrix or PFMatrixList from file. |
| GetReadsInRegion | Extract reads for each cell within a given genomic region or... |
| GetTSSPositions | Find transcriptional start sites |
| GRangesToString | GRangesToString |
| isRemote | isRemote |
| LibComplexQC | Quality control for library complexity |
| Links | Get or set links information |
| Links-set | Links |
| mergeDF | Merge two dataframe by rowname |
| MultiRegionCutMatrix | MultiRegionCutMatrix |
| PartialMatrix | PartialMatrix |
| PeakCallingFseq | Use F-seq to call peak |
| PeakCallingMACS2 | Use MACS2 to call peak |
| PeakQC | Quality control for peak overlap |
| RegionMatrix | Region enrichment analysis |
| RegionStats | Compute base composition information for genomic ranges |
| RemoveAdapter | Use AdapterRemoval to remove adapters |
| Renamer | Rename reads name in fastq |
| Returns | Return the first rows of a fragment file |
| RGo | Gene Ontology Analysis |
| RMotifScan | Search Motif Position in Given Regions |
| RMotifScanPair | Search Motif Position in Given Regions |
| RPeakAnno | Annotate ATAC-seq Peak |
| RPeakComp | Find the overlap or differential peaks between two samples. |
| RSNPs | Find whether snps are in the given regions. |
| Rsortbam | Sort bam file and rebuild bai index. |
| SamToBam | Convert sam format to bam format. |
| SamToBed | Convert SAM file to BED file |
| SCBowtie2Mapping | Use bowtie2 aligner to map reads to reference genome |
| SCCellFilter | Filtering valid single cells |
| SCFindAdapter | Use AdapterRemoval to identify adapters |
| scNucleosomeQC | Quality Control for Nucleosome Signal per Cell |
| scPlotNucleosomeQC | Plot Nucleosome signal enrichment |
| scPlotTssQC | Plot signal enrichment around TSSs |
| SCQC | Get Single Cell Pre-processing Information |
| SCRemoveAdapter | Use AdapterRemoval to remove adapters |
| SCRenamer | Rename reads name in fastq |
| SCSamToBam | Convert sam format to bam format. |
| scTssQC | Compute TSS enrichment score per cell |
| SCUnzipAndMerge | Unzip and merge fastq files |
| SetIfNull | Set a default value if an object is null |
| SingleFeatureMatrix | SingleFeatureMatrix |
| SingleFileCutMatrix | Generate matrix of integration sites |
| SingleRepReport | Final report for single group of regions |
| SplitFragments | Split fragment file by cell identities |
| StringToGRanges | StringToGRanges |
| TabixOutputToDataFrame | TabixOutputToDataFrame |
| This | Set and get cell barcode information for a 'Fragment' object |
| TSSQC | Quality control for transcription start site(TSS) reads... |
| UnzipAndMerge | Unzip and merge fastq files |
| UpdatePath | Update the file path for a Fragment object |
| ValidateCells | Validate cells present in fragment file |
| ValidateFragments | Validate Fragment object |
| ValidateHash | Validate hashes for Fragment object |
