diff --git a/README.Rmd b/README.Rmd index 4a831b21..aaae5bab 100755 --- a/README.Rmd +++ b/README.Rmd @@ -3,6 +3,10 @@ title: "tidybulk - part of tidyTranscriptomics" output: github_document --- + +[![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![R build status](https://github.com/stemangiola/tidybulk/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/stemangiola/tidybulk/actions) + + ```{r echo=FALSE} knitr::opts_chunk$set( fig.path = "man/figures/") ``` @@ -10,10 +14,6 @@ knitr::opts_chunk$set( fig.path = "man/figures/") **Brings transcriptomics to the tidyverse!** (SEO: tidy differential expression) # - - - [![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) - website: [stemangiola.github.io/tidybulk/](http://stemangiola.github.io/tidybulk/) diff --git a/README.md b/README.md index b12fa926..7f812105 100755 --- a/README.md +++ b/README.md @@ -1,15 +1,18 @@ tidybulk - part of tidyTranscriptomics ================ + + +[![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) +[![R build +status](https://github.com/stemangiola/tidybulk/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/stemangiola/tidybulk/actions) + + **Brings transcriptomics to the tidyverse\!** (SEO: tidy differential expression) # - -[![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) - - website: [stemangiola.github.io/tidybulk/](http://stemangiola.github.io/tidybulk/) @@ -450,18 +453,18 @@ tt.norm.tSNE %>% ``` ## # A tibble: 251 x 4 - ## tSNE1 tSNE2 sample Call - ## - ## 1 1.29 9.12 TCGA-A1-A0SD-01A-11R-A115-07 LumA - ## 2 0.891 -6.20 TCGA-A1-A0SF-01A-11R-A144-07 LumA - ## 3 13.7 7.86 TCGA-A1-A0SG-01A-11R-A144-07 LumA - ## 4 -6.78 7.44 TCGA-A1-A0SH-01A-11R-A084-07 LumA - ## 5 -2.85 7.10 TCGA-A1-A0SI-01A-11R-A144-07 LumB - ## 6 -5.26 -0.763 TCGA-A1-A0SJ-01A-11R-A084-07 LumA - ## 7 -9.03 -29.8 TCGA-A1-A0SK-01A-12R-A084-07 Basal - ## 8 -14.0 5.42 TCGA-A1-A0SM-01A-11R-A084-07 LumA - ## 9 -12.7 4.75 TCGA-A1-A0SN-01A-11R-A144-07 LumB - ## 10 16.4 14.6 TCGA-A1-A0SQ-01A-21R-A144-07 LumA + ## tSNE1 tSNE2 sample Call + ## + ## 1 -4.95 5.57 TCGA-A1-A0SD-01A-11R-A115-07 LumA + ## 2 6.24 -11.3 TCGA-A1-A0SF-01A-11R-A144-07 LumA + ## 3 -11.4 2.97 TCGA-A1-A0SG-01A-11R-A144-07 LumA + ## 4 -6.53 -8.35 TCGA-A1-A0SH-01A-11R-A084-07 LumA + ## 5 -7.29 -12.6 TCGA-A1-A0SI-01A-11R-A144-07 LumB + ## 6 1.78 5.05 TCGA-A1-A0SJ-01A-11R-A084-07 LumA + ## 7 28.4 -13.7 TCGA-A1-A0SK-01A-12R-A084-07 Basal + ## 8 10.1 2.78 TCGA-A1-A0SM-01A-11R-A084-07 LumA + ## 9 9.19 3.94 TCGA-A1-A0SN-01A-11R-A144-07 LumB + ## 10 -17.8 9.12 TCGA-A1-A0SQ-01A-21R-A144-07 LumA ## # … with 241 more rows ``` r @@ -866,18 +869,18 @@ tt.norm.SNN %>% ``` ## # A tibble: 251 x 5 - ## tSNE1 tSNE2 sample Call `cluster SNN` - ## - ## 1 1.29 9.12 TCGA-A1-A0SD-01A-11R-A115-07 LumA 0 - ## 2 0.891 -6.20 TCGA-A1-A0SF-01A-11R-A144-07 LumA 2 - ## 3 13.7 7.86 TCGA-A1-A0SG-01A-11R-A144-07 LumA 1 - ## 4 -6.78 7.44 TCGA-A1-A0SH-01A-11R-A084-07 LumA 0 - ## 5 -2.85 7.10 TCGA-A1-A0SI-01A-11R-A144-07 LumB 0 - ## 6 -5.26 -0.763 TCGA-A1-A0SJ-01A-11R-A084-07 LumA 1 - ## 7 -9.03 -29.8 TCGA-A1-A0SK-01A-12R-A084-07 Basal 3 - ## 8 -14.0 5.42 TCGA-A1-A0SM-01A-11R-A084-07 LumA 2 - ## 9 -12.7 4.75 TCGA-A1-A0SN-01A-11R-A144-07 LumB 2 - ## 10 16.4 14.6 TCGA-A1-A0SQ-01A-21R-A144-07 LumA 1 + ## tSNE1 tSNE2 sample Call `cluster SNN` + ## + ## 1 -4.95 5.57 TCGA-A1-A0SD-01A-11R-A115-07 LumA 0 + ## 2 6.24 -11.3 TCGA-A1-A0SF-01A-11R-A144-07 LumA 2 + ## 3 -11.4 2.97 TCGA-A1-A0SG-01A-11R-A144-07 LumA 1 + ## 4 -6.53 -8.35 TCGA-A1-A0SH-01A-11R-A084-07 LumA 0 + ## 5 -7.29 -12.6 TCGA-A1-A0SI-01A-11R-A144-07 LumB 0 + ## 6 1.78 5.05 TCGA-A1-A0SJ-01A-11R-A084-07 LumA 1 + ## 7 28.4 -13.7 TCGA-A1-A0SK-01A-12R-A084-07 Basal 3 + ## 8 10.1 2.78 TCGA-A1-A0SM-01A-11R-A084-07 LumA 2 + ## 9 9.19 3.94 TCGA-A1-A0SN-01A-11R-A144-07 LumB 2 + ## 10 -17.8 9.12 TCGA-A1-A0SQ-01A-21R-A144-07 LumA 1 ## # … with 241 more rows ``` r