Man pages for CL-CHEN-Lab/User_interface_for_Kronos_scRT
R-package and Shiny App interface for the analysis of single cell replication timing data
| AdjustCN | Corrects CN and filters cells based on AdjustPerCell output |
| AdjustPerCell | Applies diagnostic settings to PerCell dataframe |
| Assign_subpop | Splits single cell CN dataframe based on identified... |
| AverageVariability | Calculates the proportion of replicated bins in function of... |
| BackGround | Calculates median G1/G2 profile |
| BamMetrics | recover metrics from bam files |
| binning | Calculates genomic bins with GC content and mappability |
| BinRepProbPlot | Bin Replication probability plot |
| CallCNV | Calls CNV over genomic bins defined by binning |
| cat_levels | Order in which RT categories should be plot |
| Cluster_enrichment | Gene ontology on RT clusters using clusterprofiler |
| Decompress_if_needed | Checks if files are compressed and decompressed them in a... |
| diagnostic | Helps identifying parameters for scRT analysis. It opens a... |
| extractSubpop | separates S phase cells into sub-groups and calculates... |
| FastqToBam | Trims and maps reads based on Rbowtie2 |
| FilterCells | filter cells |
| find_known_sequences | Given a genomic sequence it returns the relative coordinates... |
| GenomeBinning | Bins the genome in equally sized bins |
| GM12878_Reference | GM12878 Reference RT |
| HeLa_Reference | HeLa S3 Reference RT |
| HeLa_rep1 | SingneCell RT Test object |
| HeLa_rep2 | SingneCell RT Test object |
| IdAdapters | Identifies adapters present in a fastq |
| Jeff_rep1 | SingneCell RT Test object |
| Jeff_rep2 | SingneCell RT Test object |
| KCorr_plot | Customized GGally::ggparis function |
| load_multiple_df | Loads and binds a dataframe divided in multiple files |
| MCF7 | SingneCell RT Test object |
| MCF7_Reference | MCF7 Reference RT |
| MCF7_subpop1 | SingneCell RT Test object |
| MCF7_subpop2 | SingneCell RT Test object |
| mergefastq | merges a list of fastq files into one |
| mutate_sequence | Randomly mutates the 4 nucleotides |
| Plot_bulkRT | bulk RT plots of a region of interest |
| Prepare_G1G2_phase_cells_forBinRepProb | Prepare G1/G2 phase cells for BinRepProb plots |
| Prepare_S_phase_cells_forBinRepProb | Prepare S phase cells for BinRepProb plots |
| Pre_processing | Launch Kronos scRT pre-processing |
| Processing | Launch Kronos scRT processing |
| pseudoBulkRT | calculates pseudobulk RT |
| Rebin | rebins kronos CN data (preprocessing output) |
| RebinRT | rebins RT data |
| recover_and_mutate | Given a genomic start and end recover a genomic sequence and... |
| rejoinSubpop | reverts extractSubpop |
| Replication_state | binarizes data into replicated or not replicated bins |
| reshape_and_save | Reshapes data into fastq format and save them into a file |
| rev_com | Given a genomic sequence it calculates its reverse... |
| right_format | checks whether a file contains the right number of columns... |
| RT_changes_plot | RT changes in function of ΔRT |
| RT_clustering | Hclustering to identify RT signatures |
| RT_tools | Launch Kronos RT tools |
| scCNplot | scCN plot |
| scRTplot | scRT plot of a region of interest |
| scRT_tools | Launch Kronos scRT tools |
| sequential_trimming | Sequentially trim reads |
| shell_interface | Info to set Kronos scRT for command line |
| split_into_categoreis | given an RT value (Early == 1 and Late == 0), this function... |
| split_subpop | Splits PerCell data frame based on identified sub-populations |
| String_to_Range | converts a string representing a range of values into an... |
| T25_75 | fit RT data into sigmoid function and return T25 and T75 |
| TenXtoKronos | It converts 10X Genomics data into Kronos format |
| TSNE | adds an option to set a seed in Rtsnee |
| TW_GenomeAnnotation | Annotate Variability dataframe with a customized annotation |
| Twidth | calculates twidth |
| Twidth_barplot | Twidth barplotplot |
| Twidth_extended_plot | Extended Twidth plot |
| Twidth_fit_data | calculates twidth |
| Twidth_pval | Hypothesis test between different RT categories inside a... |
| TW_RTAnnotation | Annotate Variability dataframe based on RT Categories |
| Variability | prepares variability file |
| WhoIsWho | Assigns cell cycle staging metadata |
