diff --git a/DESCRIPTION b/DESCRIPTION
index ac5d5b9..6e59d2b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,11 +3,18 @@ Type: Package
Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Version: 0.99.0
Authors@R: c(
- person(given = "Hiranyamaya",
- family = "Dash",
- role = c("cre", "aut"),
- email = "hdash.work@gmail.com",
- comment = c(ORCID = "0009-0005-5514-505X"))
+ person(given = "Hiranyamaya",
+ family = "Dash",
+ role = c("cre", "aut"),
+ email = "hdash.work@gmail.com",
+ comment = c(ORCID = "0009-0005-5514-505X")),
+ person(given="Thomas", family="Roberts",
+ email = "tomroberts.work15@gmail.com",
+ role = "aut"),
+ person(given="Nathan", family="Skene",
+ email = "nathan.skene@gmail.com",
+ role = "aut",
+ comment = c(ORCID = "0000-0002-6807-3180"))
)
Description: MotifPeeker is used to compare and analyse datasets from epigenomic
profiling methods with motif enrichment as the key benchmark.
diff --git a/README.Rmd b/README.Rmd
index 9833193..776ee0d 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -1,7 +1,7 @@
---
-title: "`r read.dcf('DESCRIPTION', fields = 'Package')[1]`"
+title: "MotifPeeker
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment"
author: "`r rworkflows::use_badges()`"
-date: "README updated: `r format( Sys.Date(), '%b-%d-%Y')`
"
+date: "Updated: `r format( Sys.Date(), '%b-%d-%Y')`
"
output:
github_document
---
@@ -15,16 +15,36 @@ owner <- strsplit(URL,"/")[[1]][4]
repo <- strsplit(URL,"/")[[1]][5]
```
-## ``r pkg``: `r gsub("\n","",title)`
-### `r gsub("\n","",description)`
+# Introduction
+
+`MotifPeeker` is used to compare and analyse datasets from epigenomic
+profiling methods with motif enrichment as the key benchmark. The package
+outputs an HTML report consisting of three sections:
+
+1. **General Metrics**: Overview of peaks-related general metrics for the
+datasets (FRiP scores, peak widths and motif-summit distances).
+2. **Known Motif Enrichment Analysis**: Statistics for the frequency of
+user-provided motifs enriched in the datasets.
+3. **De-Novo Motif Enrichment Analysis**: Statistics for the frequency of
+de-novo discovered motifs enriched in the datasets and compared with known
+motifs.
-## Installation
+# Installation
+
+`MotifPeeker` uses
+[`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
+which relies on a local install of the
+[MEME suite](https://meme-suite.org/meme/). Installation instructions can be
+found [here](https://www.bioconductor.org/packages/release/bioc/vignettes/memes/inst/doc/install_guide.html).
+
+Once the MEME suite is installed, `MotifPeeker` can be installed using the
+following code:
```R
if(!require("remotes")) install.packages("remotes")
diff --git a/README.md b/README.md
index cecbb8f..20472fb 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
-MotifPeeker
+MotifPeeker
Benchmarking Epigenomic Profiling Methods
+Using Motif Enrichment
================
[ Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.
+`MotifPeeker` is used to compare and analyse datasets from epigenomic
+profiling methods with motif enrichment as the key benchmark. The
+package outputs an HTML report consisting of three sections:
+
+1. **General Metrics**: Overview of peaks-related general metrics for
+ the datasets (FRiP scores, peak widths and motif-summit distances).
+2. **Known Motif Enrichment Analysis**: Statistics for the frequency of
+ user-provided motifs enriched in the datasets.
+3. **De-Novo Motif Enrichment Analysis**: Statistics for the frequency
+ of de-novo discovered motifs enriched in the datasets and compared
+ with known motifs.
-
+
+
+# Installation
+
+`MotifPeeker` uses
+[`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
+which relies on a local install of the [MEME
+suite](https://meme-suite.org/meme/). Installation instructions can be
+found
+[here](https://www.bioconductor.org/packages/release/bioc/vignettes/memes/inst/doc/install_guide.html).
-## Installation
+Once the MEME suite is installed, `MotifPeeker` can be installed using
+the following code:
``` r
if(!require("remotes")) install.packages("remotes")
@@ -69,19 +90,20 @@ utils::sessionInfo()
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.5 jsonlite_1.8.8 renv_1.0.7
- ## [4] compiler_4.4.1 BiocManager_1.30.23 rvcheck_0.2.1
- ## [7] scales_1.3.0 yaml_2.3.8 fastmap_1.2.0
- ## [10] here_1.0.1 ggplot2_3.5.1 R6_2.5.1
- ## [13] knitr_1.47 yulab.utils_0.1.4 tibble_3.2.1
- ## [16] desc_1.4.3 dlstats_0.1.7 rprojroot_2.0.4
- ## [19] munsell_0.5.1 pillar_1.9.0 RColorBrewer_1.1-3
- ## [22] rlang_1.1.4 utf8_1.2.4 cachem_1.1.0
- ## [25] badger_0.2.4 xfun_0.45 fs_1.6.4
- ## [28] memoise_2.0.1 cli_3.6.2 magrittr_2.0.3
- ## [31] rworkflows_1.0.1 digest_0.6.35 grid_4.4.1
- ## [34] rstudioapi_0.16.0 lifecycle_1.0.4 vctrs_0.6.5
- ## [37] evaluate_0.24.0 glue_1.7.0 data.table_1.15.4
- ## [40] fansi_1.0.6 colorspace_2.1-0 rmarkdown_2.27
- ## [43] tools_4.4.1 pkgconfig_2.0.3 htmltools_0.5.8.1
+ ## [4] dplyr_1.1.4 compiler_4.4.1 BiocManager_1.30.23
+ ## [7] tidyselect_1.2.1 rvcheck_0.2.1 scales_1.3.0
+ ## [10] yaml_2.3.8 fastmap_1.2.0 here_1.0.1
+ ## [13] ggplot2_3.5.1 R6_2.5.1 generics_0.1.3
+ ## [16] knitr_1.47 yulab.utils_0.1.4 tibble_3.2.1
+ ## [19] desc_1.4.3 dlstats_0.1.7 rprojroot_2.0.4
+ ## [22] munsell_0.5.1 pillar_1.9.0 RColorBrewer_1.1-3
+ ## [25] rlang_1.1.4 utf8_1.2.4 cachem_1.1.0
+ ## [28] badger_0.2.4 xfun_0.45 fs_1.6.4
+ ## [31] memoise_2.0.1 cli_3.6.2 magrittr_2.0.3
+ ## [34] rworkflows_1.0.1 digest_0.6.35 grid_4.4.1
+ ## [37] rstudioapi_0.16.0 lifecycle_1.0.4 vctrs_0.6.5
+ ## [40] data.table_1.15.4 evaluate_0.24.0 glue_1.7.0
+ ## [43] fansi_1.0.6 colorspace_2.1-0 rmarkdown_2.27
+ ## [46] tools_4.4.1 pkgconfig_2.0.3 htmltools_0.5.8.1