目录
- RAdded call to Sys.which to check for pandoc before running the html output and a warning if it's not available. Also updated description to exclude rmarkdown, RGraphics, and dendextend.9年前
- dataUpdating documentation, correct example data now available9年前
- execChanged default sureness to NA from 0 this way it doesn't show up in the 'Subsampling Applied' field9年前
- instfixed move5年前
- manUpdating documentation, correct example data now available9年前
- .RbuildignoreCommand line capable now. Other minor changes9年前
- .gitignorev0.1.1: Added mods variable to filecache to track subsampling done, filecacher now recreates filecache on run/load, mods added to plot, two column Inc Groups legend9年前
- .gitlab-ci.ymlReverted to the way the yml file was in the last commit9年前
- DESCRIPTIONAdd URL to DESCRIPTION4年前
- LICENSE.txtInitial commit to master9年前
- NAMESPACEUpdated palette used to Paired, added first element as black to keep the non-amr plasmids black9年前
- NOTICE.txtInitial commit to master9年前
- Plasmidprofiler.RprojRequired R version, filename treatment, rscript output filename arg added9年前
- README.mdRestructured directory, updated yml, typo fix in main_aux9年前
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Plasmid Profiler
Legal
Plasmid Profiler
Copyright Government of Canada 2015-2016
Written by: Adrian Zetner, Public Health Agency of Canada, National Microbiology Laboratory
Funded by the National Micriobiology Laboratory
Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at:
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Description
The Plasmid Profiler leverages BLAST and short read sequece typing to identify Enterobacteriaceae plasmids from NGS reads. The results are then parsed and presented in a heatmap format showing the likely plasmid families present and AMR genes discovered within the sequencing data.
Release
P2 v 0.1
Requirements
P2 requires R (>= 3.3.1)
Installation
Download R package and enter the following command
Running P2
Please refer to the documentation for more details.
Contact
Adrian Zetner: adrian.zetner@phac-aspc.gc.ca