Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / audy/richardson-2014 issues and pull requests

#57 - Problems with normalize.R

Issue - State: open - Opened by adriaaula over 8 years ago - 1 comment

#56 - update w/ audy branch for publication

Pull Request - State: closed - Opened by audy about 10 years ago

#55 - pca ~ diversity index

Issue - State: closed - Opened by audy over 10 years ago - 1 comment

#53 - add packrat files

Issue - State: closed - Opened by audy over 10 years ago

#51 - Use dplyr in place of plyr

Issue - State: open - Opened by audy over 10 years ago

#50 - Use data.table for loading CSV files (because they're quite large).

Issue - State: closed - Opened by audy over 10 years ago - 1 comment

#49 - Combine Genus and species names in species-level plots.

Issue - State: closed - Opened by audy over 10 years ago

#48 - Add figure theme

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment

#47 - Add appearance of autoantibodies to time-series plots

Issue - State: closed - Opened by audy almost 11 years ago

#46 - Add GLM to time-series analysis

Issue - State: closed - Opened by audy almost 11 years ago

#45 - Plot ROC curve for GLM

Issue - State: closed - Opened by audy almost 11 years ago

#44 - Gmulti

Pull Request - State: closed - Opened by audy almost 11 years ago

#43 - Add qPCR GLM regression

Issue - State: closed - Opened by audy almost 11 years ago
Labels: analysis, data

#42 - Fix scales in sliding window plots

Issue - State: closed - Opened by audy almost 11 years ago
Labels: bug

#41 - Add linear regression and calculate R^2 for diversity measures plot

Issue - State: open - Opened by audy almost 11 years ago
Labels: analysis

#40 - Sliding window diversity

Pull Request - State: closed - Opened by audy almost 11 years ago

#39 - The real sliding window

Pull Request - State: closed - Opened by audy almost 11 years ago

#38 - Remove (possibly) contaminated samples?

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: analysis

#37 - Re-assign taxonomies

Issue - State: closed - Opened by audy almost 11 years ago
Labels: bug, analysis, data

#36 - Comply with the MIMARKS

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: data

#35 - Sample Barcode Mapping

Issue - State: closed - Opened by audy almost 11 years ago
Labels: data

#34 - Sample Barcode Mapping

Issue - State: closed - Opened by audy almost 11 years ago - 2 comments
Labels: data

#33 - Sliding window ordination

Issue - State: closed - Opened by audy almost 11 years ago
Labels: analysis

#32 - Run sequences through QIIME 1.8

Issue - State: closed - Opened by audy almost 11 years ago
Labels: data

#31 - Independent surrogate variable analysis

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: analysis, proposal

#30 - Comply with LGPL for qvalue code

Issue - State: closed - Opened by audy almost 11 years ago
Labels: bug

#29 - Normalize using Total Bacterial Count

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: analysis, proposal

#28 - Do non time-series hypothesis testing.

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: analysis

#27 - Add test data

Issue - State: open - Opened by audy almost 11 years ago
Labels: data

#26 - Closes #24

Pull Request - State: closed - Opened by audy almost 11 years ago

#25 - Do actual SLIDING window smoothing/hypothesis testing

Issue - State: closed - Opened by audy almost 11 years ago
Labels: analysis

#24 - Fix qvalue calculation to use the # of OTUs not # OTUs * # Samples

Issue - State: closed - Opened by audy almost 11 years ago

#23 - Add FDR Corrections

Pull Request - State: closed - Opened by audy almost 11 years ago

#22 - Generate biom files

Issue - State: open - Opened by audy almost 11 years ago
Labels: enhancement

#21 - Add code to generate Wiggum plots

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: enhancement

#20 - closes #18

Pull Request - State: closed - Opened by audy almost 11 years ago

#19 - Download PICRUST precalc files in Makefile

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: bug

#18 - Correct for copy number variation

Issue - State: closed - Opened by audy almost 11 years ago

#17 - Incorporate GLMULTI code

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: enhancement

#16 - Resolves #14

Pull Request - State: closed - Opened by audy almost 11 years ago

#15 - Plot ordination

Pull Request - State: closed - Opened by audy almost 11 years ago

#14 - Load/Save phylogenetic tree

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment

#13 - Add ordination plots

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment

#12 - Add GreenGenes 97% Rep Set Tree

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment

#11 - PERMANOVA time series code.

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: analysis

#10 - Added Picrust

Pull Request - State: closed - Opened by audy almost 11 years ago

#9 - Add FDR corrections

Issue - State: closed - Opened by audy almost 11 years ago - 5 comments

#8 - Add PICRUST code

Issue - State: closed - Opened by audy almost 11 years ago

#7 - Make into a package?

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment

#6 - Add permuted t-test

Issue - State: closed - Opened by audy almost 11 years ago

#5 - Add diversity plots

Issue - State: closed - Opened by audy almost 11 years ago
Labels: enhancement

#4 - Add Python code

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment
Labels: enhancement

#3 - Add script to dump Phyloseq .RData Object

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment

#2 - Add p-values to rug in sliding window plot

Issue - State: closed - Opened by audy almost 11 years ago - 1 comment

#1 - PICRUST contributions

Issue - State: open - Opened by audy almost 11 years ago
Labels: analysis