Ecosyste.ms: Issues

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

GitHub / wejlab/BatchQC issues and pull requests

#101 - Option to select multiple variables to include in nb analysis

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

#100 - Added DeSeq2 Negative Binomial check for more than 20 samples

Pull Request - State: closed - Opened by jessmcc22 about 2 months ago

#99 - Is R > 4.4.0 really a requirement?

Issue - State: open - Opened by onurcanbektas 3 months ago

#97 - Added bladderbatch warning message if not installed

Pull Request - State: closed - Opened by jessmcc22 4 months ago

#95 - Add Ratio Statistic Functionality

Pull Request - State: closed - Opened by jessmcc22 6 months ago

#94 - Update assay name to underscores

Pull Request - State: closed - Opened by jessmcc22 7 months ago

#92 - Updated BatchQC Intro to reflect current state of shiny app

Pull Request - State: closed - Opened by jessmcc22 7 months ago

#91 - Added log only normalization option

Pull Request - State: closed - Opened by jessmcc22 7 months ago

#90 - Merge w/mani2012 BatchQC and updated bioconductor

Pull Request - State: closed - Opened by jessmcc22 7 months ago

#89 - Add original BatchQC history

Pull Request - State: closed - Opened by jessmcc22 8 months ago

#88 - Passes all R CMD and BiocCheck tests

Pull Request - State: closed - Opened by jessmcc22 8 months ago

#87 - Update differential expression function documentation

Pull Request - State: closed - Opened by jessmcc22 8 months ago

#86 - Updated Example Files to Be more accurate

Pull Request - State: closed - Opened by jessmcc22 8 months ago

#85 - Updated variation analysis

Pull Request - State: closed - Opened by jessmcc22 8 months ago

#84 - Added limma functionality

Pull Request - State: closed - Opened by jessmcc22 8 months ago

#83 - Minor changes to code structure

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

#82 - Updated heatmap plotter function with added features

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

#81 - Added checkbox to choose if data is logged for PCA and heatmap

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

#79 - Added Checkbox to Dendrogram

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

#78 - Added more examples

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

#77 - Add Checkbox to Dendrogram so users can choose if batch is leaf or text

Issue - State: closed - Opened by jessmcc22 about 1 year ago - 1 comment

#76 - Update Heatmap Coloring

Issue - State: closed - Opened by jessmcc22 about 1 year ago

#75 - Add a ReadMe file for github

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

#73 - Added Examples for Dendrogram functions

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

#72 - Updated Various Check Errors

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

#71 - Updated dendrogram plotting

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

#70 - Fixed lintr and BiocCheck errors

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

#68 - Updated Shiny app to add additional dendrogram variable

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

#67 - Fixed CRAN test problems

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

#66 - Corrected Dendrogram Labeling; Added Command line vignette info

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

#65 - Broke up R files into smaller files/functions

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

#64 - Added Vignette Info

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

#63 - Variation Analysis is Incorrect

Issue - State: closed - Opened by jessmcc22 over 1 year ago - 1 comment

#62 - Heatmap should not plot more than 500 genes

Issue - State: open - Opened by jessmcc22 over 1 year ago

#61 - Heatmap Crash w/Combat-Seq

Issue - State: open - Opened by jessmcc22 over 1 year ago

#59 - Volcano Plot not functioning w/Example Data

Issue - State: closed - Opened by jessmcc22 over 1 year ago

#57 - Added bladder data set to example options

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

#56 - updated signature data set to display meta data

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

#55 - Added Signature Data Set and started separating .R files

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

#54 - Packages getting replaced automatically

Issue - State: closed - Opened by solomonsjoseph over 1 year ago - 1 comment

#53 - Create Circular Dendogram

Issue - State: closed - Opened by jessmcc22 over 1 year ago

#52 - Break up the batch_correction.R file

Issue - State: closed - Opened by jessmcc22 over 1 year ago

#51 - Break up the plotter.R file

Issue - State: closed - Opened by jessmcc22 over 1 year ago

#50 - Add ability to clear dataset

Issue - State: open - Opened by jessmcc22 over 1 year ago

#49 - Update DataSets

Issue - State: closed - Opened by jessmcc22 over 1 year ago - 1 comment

#48 - Assess R functions from Command Line

Issue - State: closed - Opened by jessmcc22 over 1 year ago

#47 - Add CombatSeq Adjustment option

Issue - State: closed - Opened by jessmcc22 over 1 year ago

#46 - Updated volcano plot data points to be interactive

Pull Request - State: closed - Opened by evanjh19 about 2 years ago

#45 - Merge Heatmaps and Dendrograms Tabs

Issue - State: open - Opened by evanjh19 about 2 years ago

#44 - Dendrogram UI Changes

Issue - State: closed - Opened by evanjh19 about 2 years ago

#43 - Additional DE Analysis Method Options

Issue - State: closed - Opened by evanjh19 about 2 years ago - 2 comments

#42 - Volcano Plot Advanced Options

Issue - State: closed - Opened by evanjh19 about 2 years ago

#41 - Interactive Volcano Plot

Issue - State: closed - Opened by evanjh19 about 2 years ago

#40 - DE analysis tab update

Pull Request - State: closed - Opened by evanjh19 over 2 years ago

#39 - DE Analysis Tab Update

Pull Request - State: closed - Opened by evanjh19 over 2 years ago

#38 - Added download button for differential expression analysis results

Pull Request - State: closed - Opened by evanjh19 over 2 years ago

#36 - Moved dendrogram visualizations into their own tab

Pull Request - State: closed - Opened by evanjh19 over 2 years ago

#35 - Dendrograms only accept one variable input

Issue - State: closed - Opened by jessmcc22 over 2 years ago - 1 comment

#33 - Updated dendrogram visualizations, differential expression analysis v…

Pull Request - State: closed - Opened by evanjh19 over 2 years ago

#32 - Updated PCA graph to allow shape and color to plot correctly

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

#30 - Removed print lines used for testing

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

#29 - Corrected spacing; Made PCA header more visually appealing

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

#26 - Implemented DE analysis and analysis results visualization

Pull Request - State: closed - Opened by evanjh19 over 2 years ago - 1 comment

#24 - Export summarized experiment function

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

#23 - Revert "Improved dendrogram and circular dendrogram vizs."

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

#22 - Updated Example Data Input/Display

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

#21 - Corrected spacing issues in YAML code

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

#20 - Updated Code to meet BiocCheck Requirements

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

#19 - Added Protein Data Example Option

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

#18 - Improved dendrogram and circular dendrogram vizs.

Pull Request - State: closed - Opened by evanjh19 over 2 years ago

#17 - Server Files and Data Upload Options created

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

#16 - Updates to fix errors/merged

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

#15 - Revert 1 main

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

#14 - Removed data files; created documentation for remaining data file

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

#13 - Fixed some Errors/Warnings form BioConductor Tests

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

#12 - Worked on BioConductor Test Errors/Warnings

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

#11 - Prevent App Crash when User Numeric Input is invalid

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

#10 - App Crashes when user inputs are Null

Issue - State: open - Opened by jessmcc22 over 2 years ago

#7 - Added a SummarizedExperiment Object to the sample data sets

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

#6 - Data preview, data download, and usage documentation update

Pull Request - State: closed - Opened by evanjh19 over 2 years ago

#5 - Updating development changes to the main version

Pull Request - State: closed - Opened by wevanjohnson over 2 years ago

#4 - Dev package

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

#3 - Dev tabs

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