Package: PeakSegDisk 2024.10.1
PeakSegDisk: Disk-Based Constrained Change-Point Detection
Disk-based implementation of Functional Pruning Optimal Partitioning with up-down constraints <doi:10.18637/jss.v101.i10> for single-sample peak calling (independently for each sample and genomic problem), can handle huge data sets (10^7 or more).
Authors:
PeakSegDisk_2024.10.1.tar.gz
PeakSegDisk_2024.10.1.zip(r-4.5)PeakSegDisk_2024.10.1.zip(r-4.4)PeakSegDisk_2024.10.1.zip(r-4.3)
PeakSegDisk_2024.10.1.tgz(r-4.4-x86_64)PeakSegDisk_2024.10.1.tgz(r-4.4-arm64)PeakSegDisk_2024.10.1.tgz(r-4.3-x86_64)PeakSegDisk_2024.10.1.tgz(r-4.3-arm64)
PeakSegDisk_2024.10.1.tar.gz(r-4.5-noble)PeakSegDisk_2024.10.1.tar.gz(r-4.4-noble)
PeakSegDisk_2024.10.1.tgz(r-4.4-emscripten)PeakSegDisk_2024.10.1.tgz(r-4.3-emscripten)
PeakSegDisk.pdf |PeakSegDisk.html✨
PeakSegDisk/json (API)
NEWS
| # Install 'PeakSegDisk' in R: |
| install.packages('PeakSegDisk', repos = c('https://tdhock.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tdhock/peaksegdisk/issues
Last updated 2 months agofrom:7e0e474a16. Checks:OK: 1 ERROR: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win-x86_64 | ERROR | Nov 01 2024 |
| R-4.5-linux-x86_64 | ERROR | Nov 01 2024 |
| R-4.4-win-x86_64 | ERROR | Nov 01 2024 |
| R-4.4-mac-x86_64 | ERROR | Nov 01 2024 |
| R-4.4-mac-aarch64 | ERROR | Nov 01 2024 |
| R-4.3-win-x86_64 | ERROR | Nov 01 2024 |
| R-4.3-mac-x86_64 | ERROR | Nov 01 2024 |
| R-4.3-mac-aarch64 | ERROR | Nov 01 2024 |
Exports:col.name.listfread.firstfread.lastPeakSegFPOP_dfPeakSegFPOP_dirPeakSegFPOP_filePeakSegFPOP_vecsequentialSearch_dirwc2intwriteBedGraph
Dependencies:data.table
Examples
Rendered fromExamples.Rnwusingknitr::knitron Nov 01 2024.Last update: 2023-11-27
Started: 2019-07-31
Spatial correlation
Rendered fromSpatial_correlation.Rmdusingknitr::knitron Nov 01 2024.Last update: 2023-09-05
Started: 2019-07-31
Worst case time complexity
Rendered fromWorst_case.Rmdusingknitr::knitron Nov 01 2024.Last update: 2023-09-05
Started: 2019-07-31
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Reads aligned to hg19 from two ChIP-seq experiments | ChIPreads |
| coef PeakSegFPOP df | coef.PeakSegFPOP_df |
| coef PeakSegFPOP dir | coef.PeakSegFPOP_dir |
| col name list | col.name.list |
| Quickly read first line | fread.first |
| Quickly read last line | fread.last |
| A small ChIP-seq data set in which peaks can be found using PeakSegFPOP | Mono27ac |
| PeakSeg penalized solver for data.frame | PeakSegFPOP_df |
| PeakSeg penalized solver with caching | PeakSegDisk PeakSegFPOP_dir |
| PeakSegFPOP using disk storage | PeakSegFPOP_file |
| PeakSeg penalized solver for integer vector | PeakSegFPOP_vec |
| plot PeakSegFPOP df | plot.PeakSegFPOP_df |
| plot PeakSegFPOP dir | plot.PeakSegFPOP_dir |
| Compute PeakSeg model with given number of peaks | sequentialSearch_dir |
| summary PeakSegFPOP dir | summary.PeakSegFPOP_dir |
| wc2int | wc2int |
| Write bedGraph file | writeBedGraph |
