Provenance:
- URL: https://github.com/riboviz/riboviz
- Date: 08/09/2021
- Branch: develop
- Commit: c0c9911
Environment:
| Command-line tool | Version |
|---|---|
| Git | 2.17.1 |
| cURL | 7.69.1 |
| bedtools | 2.26.0 |
| hdf5tools (h5diff) | 1.10.6 |
| pigz | 2.4 |
| pandoc | 1.19.2.4 |
| GraphViz (dot) | 2.40.1 |
| zip | 3.0 |
| unzip | 6.00 |
| R | 3.6.3 |
| Python | 3.7.6 |
| Cutadapt | 1.18 |
| samtools | 1.9 |
| UMI-tools | 1.0.1 |
| Java (javac) | 1.8.0_152-release |
| Java (java) | 1.8.0_152-release |
| Nextflow | 20.04.1.5335 |
| Hisat2 | 2.1.0 |
| Bowtie | 1.2.2 |
| R Package | Version |
|---|---|
| Biostrings | 2.54.0 |
| devtools | 2.3.2 |
| git2r | 0.27.1 |
| glue | 1.4.1 |
| here | 1.0.1 |
| knitr | 1.33 |
| lintr | 2.0.1 |
| optparse | 1.6.6 |
| plotly | 4.9.2.1 |
| RcppRoll | 0.3.0 |
| rhdf5 | 2.30.1 |
| rmarkdown | 2.7 |
| roxygen2 | 7.1.1 |
| Rsamtools | 2.2.3 |
| rtracklayer | 1.46.0 |
| shiny | 1.5.0 |
| ShortRead | 1.44.3 |
| styler | 1.3.2 |
| testthat | 3.0.1 |
| tidyverse | 1.3.0 |
| withr | 2.3.0 |
| Python Package | Version | Package Manager |
|---|---|---|
| biopython | 1.77 | conda |
| cutadapt | 1.18 | conda |
| gffutils | 0.10.1 | conda |
| gitpython | 3.1.3 | conda |
| h5py | 2.10.0 | conda |
| nextflow | 20.04.1 | conda |
| pandas | 1.0.5 | conda |
| pycodestyle | 2.6.0 | conda |
| pylint | 2.5.3 | conda |
| pysam | 0.15.3 | conda |
| pytest | 5.4.3 | conda |
| pytest-cov | 2.10.1 | conda |
| pyyaml | 5.3.1 | conda |
| samtools | 1.9 | conda |
| sphinx | 4.0.1 | conda |
| umi_tools | 1.0.1 | conda |