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Add reference page and vignettes for pkgdown site (#56) #56

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Jan 5, 2019
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42d0203
Initial commit of package docs.
grabear Dec 28, 2018
995507a
Added initial description.
grabear Dec 28, 2018
d1efc7d
Updated with details section.
grabear Dec 28, 2018
6ec1388
Updated bad NAMESPACE imports.
grabear Dec 28, 2018
d780a4c
Added Other Documentation section to package docs.
grabear Dec 28, 2018
df79e96
updated NAMESPACE
grabear Dec 28, 2018
fbe4d30
Started vignettes setup.
grabear Dec 28, 2018
a30a949
Started vignettes setup.
grabear Dec 28, 2018
66f4ec7
Initialized introduction vignette.
grabear Dec 28, 2018
8e56c91
Added MicrobiomeR Formats section to the introduction vignette.
grabear Dec 28, 2018
090d7da
Added start to the data-wrangling vignette.
grabear Dec 28, 2018
08dc65e
Updated the data-wrangling vignette.
grabear Dec 28, 2018
ee69d3c
Updated docs.
grabear Dec 28, 2018
7454fc3
Made a function for creating a rooted phylogenetic tree from a phylos…
grabear Dec 31, 2018
7dd0031
Updated the roxygen documentation for the new function.
grabear Dec 31, 2018
c63bfa5
Updated the get_phyloseq_obj function.
grabear Dec 31, 2018
c891168
Added an import section to the data-wrangling vignette.
grabear Dec 31, 2018
432298f
Added a Formatting section to the data-wrangling vignette.
grabear Dec 31, 2018
c075590
Updated data-wrangling vignette.
grabear Dec 31, 2018
7783d4a
Updated introduction vignette.
grabear Dec 31, 2018
53c8ec3
Added initial commit to workflow vignette.
grabear Dec 31, 2018
ad4d19a
Added a Data Wrangling section to the workflow vignette.
grabear Dec 31, 2018
50b0ecd
Added a Basic Filtering section to the workflow vignette.
grabear Dec 31, 2018
df25902
Added the Advanced Filtering section to the workflow vignette.
grabear Dec 31, 2018
345f508
Renamed workflow vignette to filtering vignette.
grabear Dec 31, 2018
3e3a0fd
Added some minor fixes to vignette docs.
grabear Jan 2, 2019
3b04153
Updated bug in transposer function.
grabear Jan 2, 2019
b4a633f
Added the Other Filtering section.
grabear Jan 2, 2019
ed09379
Added the Transposing subsection.
grabear Jan 2, 2019
5964418
Updated transformer function.
grabear Jan 2, 2019
72e1be9
Added the Transforming subsection.
grabear Jan 2, 2019
70b96ce
Updated vlookup function with more pragmatic parameter names.
grabear Jan 2, 2019
01e93df
Added Vlookup sub section, and reformatted other sections.
grabear Jan 2, 2019
813ab4e
Initial commit of analysis vignette.
grabear Jan 2, 2019
859da31
Added Data Wrangling section to analysis vignette.
grabear Jan 2, 2019
aa793f0
Added Filtering section to analysis vignette.
grabear Jan 2, 2019
5577c6e
Added the Statistics sub-section, and updated the Analysis overview.
grabear Jan 2, 2019
fcd9f32
Fixed get_output_dir logic flow.
grabear Jan 2, 2019
0ac7fb8
Added output message for corr-plot generation, and added palette cust…
grabear Jan 3, 2019
38b76c1
Fixed palette bugs and added the rev parameter to get_color_palette f…
grabear Jan 3, 2019
7de073c
Added a Visualization sub-section to the analysis vignette.
grabear Jan 3, 2019
ac774bd
Updated package after build and install.
grabear Jan 3, 2019
bd78e8a
Merge pull request #55 from vallenderlab/dev-master
grabear Jan 3, 2019
30eec65
Fixed inconsistent @family names.
grabear Jan 4, 2019
33e1d2a
Removed get-started vignette.
grabear Jan 4, 2019
0cb39f5
Made relevent updates including adding the Data Import reference sect…
grabear Jan 4, 2019
64bfb02
Added the Data Formatting reference section.
grabear Jan 4, 2019
b396565
Updated reference sections using has_concept to identify family of fu…
grabear Jan 4, 2019
b484aba
Added Validation reference section.
grabear Jan 4, 2019
5ef635a
Added Filtering reference section.
grabear Jan 4, 2019
5adb643
Fixed spelling error in data-wrangling vignette.
grabear Jan 4, 2019
f7007af
Added Visualization reference section.
grabear Jan 4, 2019
d315e9c
Fixed bug.
grabear Jan 4, 2019
10f4d4a
Updated package after build and install.
grabear Jan 4, 2019
28d87bb
Bumped version to 0.1.4
grabear Jan 4, 2019
2b20fda
Added a NEWS section for 0.1.4
grabear Jan 4, 2019
9f7aefc
Updated README.
grabear Jan 4, 2019
b1fd853
Updated analysis vignette.
grabear Jan 4, 2019
731f281
Changed sample_filter function, and updated the @family tags.
grabear Jan 4, 2019
5e4bf25
Bumped to 0.2.3.
grabear Jan 4, 2019
69185c4
Reverted to 0.2.0.
grabear Jan 4, 2019
c28ce5d
Changed get_phyloseq_obj to create_phyloseq.
grabear Jan 4, 2019
8d279a2
Converted get_phyloseq_obj to create_phyloseq.
grabear Jan 4, 2019
ddb4935
Updated pkgdown.
grabear Jan 4, 2019
f46905c
Added Visualization family to save_barplot function.
grabear Jan 4, 2019
54f11b9
Reorganized formatting functions and changed format_mc_obj to as_cust…
grabear Jan 4, 2019
84f5ed1
Added the Formatting family to the MicrobiomeR_Formats section.
grabear Jan 4, 2019
f3b0a8e
Fixed roxygen build bugs.
grabear Jan 4, 2019
8cde9b7
Updated roxygen for heat-tree.
grabear Jan 4, 2019
bd7bfe9
Updated NEWS.md.
grabear Jan 5, 2019
2f6cd2f
Fixed build errors.
grabear Jan 5, 2019
d055579
Added built pkgdown site.
grabear Jan 5, 2019
2c9840a
Added about and color-palette vignettes.
grabear Jan 5, 2019
6c51a64
Updated package after build and install.
grabear Jan 5, 2019
784fa3f
Added missing dependecies.
grabear Jan 5, 2019
b469eb2
Update README.md
sdhutchins Jan 5, 2019
4398800
Update NEWS.md
sdhutchins Jan 5, 2019
d6a7882
Update R/phyloseq.R
sdhutchins Jan 5, 2019
48e2a6b
Update R/phyloseq.R
sdhutchins Jan 5, 2019
108f73f
Updated package after build and install.
grabear Jan 5, 2019
203ed6b
Updated pkgdown after build_site
grabear Jan 5, 2019
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Updated README.
grabear committed Jan 4, 2019
commit 9f7aefc5d9fedf3a06d3bce15ed336316cfcf15d
43 changes: 27 additions & 16 deletions README.md
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# MicrobiomeR

An R package for microbiome analysis combining the `phyloseq`, `metacodeR`, and `microbiome` packages into an easy to use and full featured microbiome analysis package.

## Features

- Standardization of data processing.
- Phyloseq for data import.
- MicrobiomeR for data validation and preprocessing.
- Metacoder for data analysis.
- Ggplot2 for data visualization.
- Publication ready figures for various ranks.
- Metacoder Heat Trees
- MicrobiomeR Correlation Plots
- MicrobiomeR Stacked Bar Charts
- Easily access taxonomic ranks from data objects.
- Import various data types from different pipelines.
An R package for microbiome analysis that incorporates [phyloseq](https://github.com/joey711/phyloseq),
[metacoder](https://github.com/grunwaldlab/metacoder), [taxa](https://github.com/ropensci/taxa), and [microbiome](https://github.com/microbiome/microbiome/) into a fully featured bioinformatics workflow.
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## Installation

We are currently not on CRAN or Bioconductor:

```r
install.packages("MicrobiomeR")
library(devtools) # Load the devtools package
install_github("vallenderlab/MicrobiomeR") # Install the package
```

## Workflow Features

- Standardization of data wrangling.
- Phyloseq for data import.
- Taxa for the primary data object (**Taxmap**).
- Proprietary data formatting and validation.
- Phyloseq inspired filtering for `taxa::taxmap` objects.
- Metacoder/taxa for mainstream filtering.
- Proprietary basic filtering for samples, taxonomies, and OTUs.
- Proprietary advanced filtering (phyloseq-style).
- Other Proprietary filtering functions for observation data.
- Metacoder enabled statistical analysis functions.
- Various visualization options.
- Output Directories
- Color Palettes
- Heat Trees
- Correlation Plots
- Stacked Bar Plot
- Alpha Diversity Plot
- Ordination Plot

## Notes

* Code Style based on Google's R style developed by Hadley Wickham.