wejlab/animalcules issues and pull requests

#70 - Maximum Upload Size Exceeded

Issue - State: open - Opened by IdanBanson 7 months ago

#69 - Unknown "V1" taxa in abundance taxa plot

Issue - State: open - Opened by IdanBanson 10 months ago - 6 comments

#68 - Fixed reading in files from a directory that has more than just patho counts files in the directory

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#67 - Updated to reflect online documentation

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#66 - Update image location for documentation

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#65 - compiled NMDs changes

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#64 - Added documentation for diversity NMDS plot

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#63 - Corrected Select input for beta diversity NMDS covariates so that it …

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#62 - updated "compbiomed" references to "wejlab"

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#61 - NMDS passes all checks

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#60 - update devel version number

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#59 - Updated to depend on R version 4.3.0; added "glmnet" pacakge to sugsts; updated websites in description to reflect github switch from compbiomed to wejlab

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#58 - Update version number properly

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#57 - added Jessica as maintainer

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#56 - update version merge conflict

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#55 - updated deprecated aes_string to aes, corrected global variable warning;

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#54 - Updated devtools install

Pull Request - State: closed - Opened by jessmcc22 about 1 year ago

#53 - BIOM file upload brings out error

Issue - State: closed - Opened by IdanBanson over 1 year ago - 2 comments

#52 - Fixed BioConductor Warnings

Pull Request - State: closed - Opened by jessmcc22 almost 2 years ago

#51 - No species level option available

Issue - State: open - Opened by nunrath over 2 years ago - 1 comment

#50 - lazy-load database ... PathoStat.rdb is corrupt

Issue - State: closed - Opened by ReneKat over 2 years ago - 3 comments

#49 - Quick fix for read_pathoscope_data()

Issue - State: closed - Opened by aubreyodom almost 3 years ago - 1 comment

#48 - Workflow separations & Correlation Analysis

Pull Request - State: open - Opened by sktpndt97 over 3 years ago

#47 - Update to include Workflow separations & correlation analysis

Pull Request - State: closed - Opened by sktpndt97 over 3 years ago

#46 - Is Alpha rarefaction required?

Issue - State: closed - Opened by s6aamani almost 4 years ago - 1 comment

#45 - Updating to include Workflow separations + correlation analysis

Pull Request - State: closed - Opened by sktpndt97 almost 4 years ago

#44 - Incorrect options for Select Target Condition in Biomarker Analysis

Issue - State: closed - Opened by jarrodscott almost 4 years ago - 2 comments

#43 - Counts file - only relative abundance data

Issue - State: closed - Opened by davitero over 4 years ago - 2 comments

#42 - categorized variables need to be as.character()

Issue - State: closed - Opened by jasonzhao0307 almost 5 years ago

#41 - Adjustable graph size

Issue - State: closed - Opened by Zinthrow almost 6 years ago
Labels: enhancement

#40 - X11 colors in the barplots area?

Issue - State: closed - Opened by Zinthrow almost 6 years ago
Labels: enhancement

#39 - Biomarker names cannot handle spaces

Issue - State: closed - Opened by Zinthrow almost 6 years ago - 2 comments

#38 - Import from phyloseq?

Issue - State: closed - Opened by cjfields almost 6 years ago - 3 comments

#37 - linux check error related to Entrez

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago - 3 comments

#36 - bioc

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#35 - Bioconductor Reviews

Issue - State: closed - Opened by anfederico almost 6 years ago

#34 - add detail explanation for each button/option in the screen shot

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago - 4 comments

#33 - add testthat

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#32 - Summary plot below error

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago - 1 comment

#31 - Alpha diversity plot continuous dot plot

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago - 1 comment

#30 - Modify tSNE (save the tSNE result to an assay)

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#29 - Modify differential abundance analysis

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago - 1 comment

#28 - add Limma to Differential abundance analysis using logCPM

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#27 - logCPM set to default assay for PCA

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#26 - modify the Boxplot in Abundance

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#25 - Add species level to animalcules

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#24 - Add a new assay dashboard sub-tab in the "Summary and Filter" tab

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#23 - Microbe filter modify

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#22 - Check/Fix summary statistics

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#21 - Complete docs (figures, descriptions, TOC)

Issue - State: closed - Opened by jasonzhao0307 almost 6 years ago

#20 - Add more distance metrics for PCoA

Issue - State: closed - Opened by anfederico about 6 years ago

#19 - resolve biocCheck warnings and notes

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#18 - Output vignette to GitHub-compatible README

Issue - State: closed - Opened by anfederico about 6 years ago

#17 - package size NOTE

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#16 - Fix devtools:check() run time too long issue

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago - 5 comments

#15 - add a logo

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago - 1 comment

#14 - Fix the building errors

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#13 - modify DE

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#12 - Check all figures, make sure the y-axis and x-axis name makes sense to users

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#11 - Change the PCoA 1st and 2nd option name to principle coordinate instead of principle components

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#10 - Make the Mann Whitney test name consistent for the stat result table name

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#9 - Add a ROC plot to biomarker page

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#8 - Add t-SNE and Umap to dim reduction page

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#7 - Make default tax level being phylum

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#6 - Make each page as simple as possible

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago

#5 - Add one or two more example datasets and user could select which example dataset to use

Issue - State: closed - Opened by jasonzhao0307 about 6 years ago
Labels: enhancement

#4 - Here are some changes to help R CMD CHECK work, but there still are some changes needed

Pull Request - State: closed - Opened by wevanjohnson about 6 years ago

#3 - Fixing some errors on the alignment function (and other functions) that caused R CMD CHECK to fail. I think there are some examples that still fail from others

Pull Request - State: closed - Opened by wevanjohnson about 6 years ago - 1 comment

#2 - Adding changes to the demultiplex functions and adding functions for …

Pull Request - State: closed - Opened by wevanjohnson about 6 years ago

#1 - Adding function for refseq reference library download

Pull Request - State: closed - Opened by wevanjohnson about 6 years ago

GitHub / wejlab/animalcules issues and pull requests