Mercurial > repos > george-weingart > maaslin
annotate maaslin-4450aa4ecc84/maaslin.xml @ 1:a87d5a5f2776
Uploaded the version running on the prod server
author | george-weingart |
---|---|
date | Sun, 08 Feb 2015 23:08:38 -0500 |
parents | |
children |
rev | line source |
---|---|
1
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
1 <tool id="maaslin_run" name="MaAsLin" version="1.0.1"> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
2 <code file="maaslin_format_input_selector.py"/> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
3 <description></description> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
4 <command interpreter="python">maaslin_wrapper.py |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
5 --lastmeta $cls_x |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
6 --input $inp_data |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
7 --output $out_file1 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
8 --alpha $alpha |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
9 --min_abd $min_abd |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
10 --min_samp $min_samp |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
11 --zip_file $zip_file |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
12 --tool_option1 $tool_option1 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
13 </command> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
14 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
15 <inputs> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
16 <param format="maaslin" name="inp_data" type="data" label="pcl file of metadata and microbial community measurements: Upload using Get Data-Upload file - Use File-Format = maaslin - Sample file below"/> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
17 <param name="cls_x" type="select" label="Last metadata row (Select 'Weight' for demo data set)" multiple="False" size ="70" dynamic_options="get_cols(inp_data,'0')"/> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
18 <param name="alpha" type="float" size="8" value="0.05" label="Maximum false discovery rate (significance threshold)"/> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
19 <param name="min_abd" type="float" size="8" value="0.0001" label="Minimum for feature relative abundance filtering"/> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
20 <param name="min_samp" type="float" size="8" value="0.01" label="Minimum for feature prevalence filtering"/> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
21 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
22 <param name="tool_option1" type="select" label="Type of output"> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
23 <option value="1">Single File: Summary</option> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
24 <option value="2">Two Files: Complete zipped results + Summary</option> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
25 </param> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
26 </inputs> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
27 <outputs> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
28 <data format="tabular" name="out_file1" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
29 <data name="zip_file" format="zip"> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
30 <filter>tool_option1 == "2"</filter> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
31 </data> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
32 </outputs> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
33 <requirements> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
34 <requirement type="set_environment">maaslin_SCRIPT_PATH</requirement> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
35 </requirements> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
36 <tests> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
37 <test> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
38 <param name="inp_data" value="maaslin_input" ftype="maaslin" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
39 <param name="cls_x" value="9" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
40 <param name="alpha" value="0.05" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
41 <param name="min_abd" value="0.0001" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
42 <param name="min_samp" value="0.01" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
43 <param name="tool_option1" value="1" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
44 <output name="out_file1" file="maaslin_output" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
45 <assert_contents> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
46 <has_text text="Variable Feature Value Coefficient N N.not.0 P.value Q.value" /> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
47 </assert_contents> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
48 </test> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
49 </tests> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
50 <help> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
51 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
52 Feedback? Not working? Please contact us at Maaslin_google_group_ . |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
53 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
54 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
55 MaAsLin: Multivariate Analysis by Linear Models |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
56 ----------------------------------------------- |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
57 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
58 MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and microbial community abundance or function. The clinical metadata can be of any type continuous (for example age and weight), boolean (sex, stool/biopsy), or discrete/factor (cohort groupings and phenotypes). MaAsLin is best used in the case when you are associating many metadata with microbial measurements. When this is the case each metadatum can be a diffrent type. For example, you could include age, weight, sex, cohort and phenotype in the same input file to be analyzed in the same MaAsLin run. The microbial measurements are expected to be normalized before using MaAsLin and so are proportional data ranging from 0 to 1.0. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
59 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
60 The results of a MaAsLin run are the association of a specific microbial community member with metadata. These associations are without the influence of the other metadata in the study. There are certain factors known that can influence the microbiome (for example diet, age, geography, fecal or biopsy sample origin). MaAsLin allows one to detect the effect of a metadata, possibly a phenotype, deconfounding the effects of diet, age, sample origin or any other metadata captured in the study! |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
61 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
62 .. image:: https://bytebucket.org/biobakery/galaxy_maaslin/wiki/Figure1-Overview.png |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
63 :height: 500 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
64 :width: 600 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
65 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
66 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
67 *Maaslin Analysis Overview* MaAsLin performs boosted, additive general linear models between one group of data (metadata/the predictors) and another group (in our case microbial abundance/the response). Given that metagenomic data is sparse, the boosting is used to select metadata that show some potential to be associated with microbial abundances. Boosting of metadata and selection of a model occurs per otu. The metadata data that is selected for use by boosting is then used in a general linear model using metadata as predictors and otu arcsin-square root transformed abundance as the response. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
68 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
69 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
70 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
71 For more information on the technical aspects to this algorithm please see the methodological evaluation of MaAsLin that compared it to multiviariate and univariate analyses. Please check back for paper citing. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
72 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
73 Process: |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
74 -------- |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
75 The first step consists of uploading your data using Galaxy's **Get Data - Upload File** |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
76 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
77 A sample file is located at: https://bytebucket.org/biobakery/maaslin/wiki/maaslin_demo_pcl.txt |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
78 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
79 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
80 **Important** |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
81 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
82 Please make sure to choose **File Format: maaslin** |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
83 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
84 Required inputs |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
85 --------------- |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
86 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
87 MaAsLin requires an input pcl file of metadata and microbial community measurements. MaAsLin expects a PCL file as an input file. A PCL file is a text delimited file similar to an excel spread sheet with the following characteristics. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
88 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
89 1. **Rows** represent metadata and features (bugs), **columns** represent samples |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
90 2. The **first row** by default should be the sample ids. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
91 3. Metadata rows should be next. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
92 4. Lastly, rows containing features (bugs) measurements (like abundance) should be after metadata rows. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
93 5. The **first column** should contain the ID describing the column. For metadata this may be, for example, ''Age'' for a row containing the age of the patients donating the samples. For measurements, this should be the feature name (bug name). |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
94 6. The file is expected to be TAB delimited. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
95 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
96 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
97 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
98 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
99 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
100 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
101 Description of parameters |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
102 ------------------------- |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
103 **Input file** Select a loaded data file to use in analysis. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
104 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
105 **Last metadata row** Metadata and microbial measurements should be rows of the pcl file. Metadata should all come before microbial measurements. This row is the last metadata row which is only followed by rows which are microbial measurements. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
106 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
107 **Maximum false discovery rate (Significance threshold)** Associations are found significant if thier q-value is equal to or less than this threshold. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
108 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
109 **Minimum for feature relative abundance filtering** The minimum relative abundance allowed in the data. Values below this are removed and imputed as the median of the sample data. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
110 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
111 **Minimum for feature prevalence filtering** The minimum percentage of samples a feature can have abudance in before being removed. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
112 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
113 **Type of Output** Select one of the two options for output (summary or detailed results). |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
114 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
115 Outputs |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
116 ------- |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
117 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
118 The Run MaAsLin module will create either A) a summary text file of plotted significant associations or B) a compressed directory of associations (significant and not significant). |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
119 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
120 A. Any association that had a q-value less than or equal to the significance threshold will be included in a tab-delimited file. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
121 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
122 B. The following files will be generated per MaAsLin run. In the following listing the term projectname refers to what you named your pcl file without the extension. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
123 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
124 **Analysis** (These files are useful for analysis): |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
125 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
126 **projectname-metadata.txt** Each metadata will have a file of associations. Any associations indicated to be performed after initial boosting is recorded here. Included are the information from the final general linear model (performed after the boosting) and the FDR corrected p-value (q-value). Can be opened as a text file or spreadsheet. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
127 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
128 **projectname-metadata.pdf** Any association that had a q-value less than or equal to the significance threshold will be plotted here. If this file does not exist, the projectname-metadata.txt should not have an entry that is less than or equal to the threshold. Factor and boolean data is plotted as knotched box plots; continuous data is plotted as a scatter plot with a line of best fit. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
129 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
130 .. image:: https://bytebucket.org/biobakery/galaxy_maaslin/wiki/Maaslin_Output.png |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
131 :height: 500 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
132 :width: 600 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
133 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
134 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
135 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
136 *Example of the projectname-metadata.pdf file* Significant associations are combined in files of associations per metadata. Factor and boolean data is plotted as knotched box plots; continuous data is plotted as a scatter plot with a line of best fit. Plots show raw data, header data show information from the reduced |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
137 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
138 **projectname_Summary.txt** Any entry in the projectname-metadata.pdf are collected together here. Can be opened as a text file or spreadsheet. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
139 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
140 **Troubleshooting** (These files are typically not used for analysis but are there for documenting the process and troubleshooting): |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
141 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
142 **projectname.txt** Contains the detail for the statistical engine. Is useful for detailed troubleshooting. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
143 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
144 **data.tsv** The data matrix that was read in (transposed). Useful for making sure the correct data was read in. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
145 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
146 **data.read.config** Can be used to read in the data.tsv . |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
147 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
148 **metadata.tsv** The metadata that was read in (transposed). Useful for making sure the correct metadata was read in. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
149 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
150 **metadata.read.config** Can be used to read in the data.tsv . |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
151 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
152 **read_merged.tsv** The data and metadata merged (transposed). Useful for making sure the merging occurred correctly. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
153 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
154 **read_merged.read.config** Can be used to read in the read_merged.tsv . |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
155 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
156 **read_cleaned.tsv** The data read in, merged, and then cleaned. After this process the data is written to this file for reference if needed. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
157 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
158 **read_cleaned.read.config** Can be used to read in read_cleaned.tsv . |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
159 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
160 **ProcessQC.txt** Contains quality control for the MaAsLin analysis. This includes information on the magnitude of outlier removal. |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
161 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
162 Contacts |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
163 -------- |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
164 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
165 Please feel free to contact us at ttickle@hsph.harvard.edu for any questions or comments! |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
166 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
167 .. _Maaslin_google_group: https://groups.google.com/d/forum/maaslin-users |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
168 |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
169 </help> |
a87d5a5f2776
Uploaded the version running on the prod server
george-weingart
parents:
diff
changeset
|
170 </tool> |