Last updated: 2020-10-27

Checks: 2 0

Knit directory: misc/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 5a6cc2a. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/bayeslogit.md
    Untracked:  analysis/polya_gamma.md
    Untracked:  code/kowal2019code/
    Untracked:  code/logistic.R

Unstaged changes:
    Modified:   analysis/test_typora.md

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 5a6cc2a DongyueXie 2020-10-27 wflow_publish(c(“analysis/index.Rmd”, “analysis/kl.Rmd”, “analysis/polya_gamma.Rmd”,
html ad77968 DongyueXie 2020-09-24 Build site.
Rmd ba13140 DongyueXie 2020-09-24 wflow_publish(“analysis/index.Rmd”)
html 1c05bce DongyueXie 2020-09-24 Build site.
Rmd 142074b DongyueXie 2020-09-24 wflow_publish(“analysis/index.Rmd”)
html 22ea1c8 DongyueXie 2020-09-23 Build site.
Rmd d2b54b1 DongyueXie 2020-09-23 wflow_publish(c(“analysis/index.Rmd”, “analysis/genelength.Rmd”,
html a03f840 DongyueXie 2020-09-21 Build site.
Rmd bd4a4c8 DongyueXie 2020-09-21 wflow_publish(c(“analysis/contrainedclustering.Rmd”, “analysis/count.Rmd”,
html eb32629 DongyueXie 2020-09-21 Build site.
Rmd 241207b DongyueXie 2020-09-21 wflow_publish(c(“analysis/index.Rmd”, “analysis/polya_gamma.Rmd”,
html 248219c DongyueXie 2020-06-09 Build site.
Rmd ab99bdc DongyueXie 2020-06-09 wflow_publish(“analysis/index.Rmd”)
html ffd8fca DongyueXie 2020-04-26 Build site.
Rmd bbae3fd DongyueXie 2020-04-26 wflow_publish(“analysis/index.Rmd”)
html 79483af DongyueXie 2020-04-25 Build site.
Rmd 497aba7 DongyueXie 2020-04-25 wflow_publish(“analysis/index.Rmd”)
html 5f9797b DongyueXie 2020-04-15 Build site.
Rmd d293712 DongyueXie 2020-04-15 wflow_publish(“analysis/index.Rmd”)
html c125b0b DongyueXie 2020-04-13 Build site.
Rmd 534716d DongyueXie 2020-04-13 wflow_publish(“analysis/index.Rmd”)
html a894725 DongyueXie 2020-03-21 Build site.
Rmd b4ee408 DongyueXie 2020-03-21 wflow_publish(“analysis/index.Rmd”)
html 23bc977 DongyueXie 2020-03-21 Build site.
Rmd c58a029 DongyueXie 2020-03-21 wflow_publish(“analysis/index.Rmd”)
html ece3230 DongyueXie 2020-03-12 Build site.
Rmd cb62560 DongyueXie 2020-03-12 wflow_publish(“analysis/index.Rmd”)
html 6bf0195 DongyueXie 2020-03-12 Build site.
Rmd 49b251f DongyueXie 2020-03-12 wflow_publish(“analysis/index.Rmd”)
html 28de056 DongyueXie 2020-03-08 Build site.
Rmd 54eb020 DongyueXie 2020-03-08 wflow_publish(“analysis/index.Rmd”)
html 38a46c6 DongyueXie 2020-03-04 Build site.
Rmd 9abde45 DongyueXie 2020-03-04 wflow_publish(“analysis/index.Rmd”)
html 2f6c035 Dongyue Xie 2020-02-28 Build site.
Rmd 7d207c2 Dongyue Xie 2020-02-28 wflow_publish(“analysis/index.Rmd”)
html dfa7cf4 DongyueXie 2020-02-28 Build site.
Rmd 49fc479 DongyueXie 2020-02-28 wflow_publish(“analysis/index.Rmd”)
html 5a00d9d DongyueXie 2020-02-26 Build site.
Rmd ed6ec57 DongyueXie 2020-02-26 wflow_publish(“analysis/index.Rmd”)
html a5a9e1f Dongyue Xie 2020-01-23 Build site.
Rmd afc6dec Dongyue Xie 2020-01-23 wflow_publish(“analysis/index.Rmd”)
html d4e4bc5 DongyueXie 2020-01-18 Build site.
Rmd 6490f57 DongyueXie 2020-01-18 wflow_publish(“analysis/index.Rmd”)
html 45297f2 Dongyue Xie 2020-01-16 Build site.
Rmd 2263ca9 Dongyue Xie 2020-01-16 wflow_publish(“analysis/index.Rmd”)
html a847e0a Dongyue Xie 2020-01-15 Build site.
Rmd 7f8634d Dongyue Xie 2020-01-15 wflow_publish(“analysis/index.Rmd”)
html f4e7c41 Dongyue Xie 2019-12-06 Build site.
Rmd 4f75975 Dongyue Xie 2019-12-06 wflow_publish(“analysis/index.Rmd”)
html 1dacad0 Dongyue Xie 2019-11-22 Build site.
Rmd 7b4a21f Dongyue Xie 2019-11-22 Start workflowr project.

Data Collection

RNA-Seq data collection

Pre-process pbmc data

Methods

count data analysis

kl-divergence

voom-limma

mash

ruv

Negative Bionomial distribution

Bayes GLM

EM ridge

Polya-gamma augmentation

constrained clustering

Testing by betting, p-value, BF…

Book

bayesian data analysis

Papers

MAST

mouthwash

susie summary

cisTopic scATAC-Seq

Integer‐valued functional data analysis for measles forecasting

Conditionally conjugate mean–field variational Bayes for logistic models

SymSim

RNA Velocity