From 41415a0f715a7f628f1d4d9afe38bae00ce0f131 Mon Sep 17 00:00:00 2001 From: HajkD Date: Sun, 3 Feb 2019 12:35:50 +0000 Subject: [PATCH] update README --- README.md | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8b00b128..74904f05 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,8 @@ This package is born out of my own frustration to automate the genomic data retr I happily welcome anyone who wishes to contribute to this project :) Just drop me an email. +Please find a detailed [documentation here](https://ropensci.github.io/biomartr/articles/). + ### Short package description: The vastly growing number of sequenced genomes allows us to perform a new type of biological research. @@ -35,7 +37,16 @@ In detail, `biomartr` automates genome, proteome, CDS, RNA, Repeats, GFF/GTF (an - [ENSEMBLGENOMES](http://ensemblgenomes.org) - [UniProt](http://www.uniprot.org) -Furthermore, an interface to the [Ensembl Biomart](www.ensembl.org/biomart) database allows users to retrieve functional annotation for genomic loci using a novel and organism centric search strategy. In addition, users can [download entire databases](https://github.com/HajkD/biomartr/blob/master/vignettes/Database_Retrieval.Rmd) such as `NCBI RefSeq`, `NCBI nr`, `NCBI nt`, `NCBI Genbank`, etc. as well as `ENSEMBL` and `ENSEMBLGENOMES` with only one command. +Furthermore, an interface to the [Ensembl Biomart](www.ensembl.org/biomart) database allows users to retrieve functional annotation for genomic loci using a novel and organism centric search strategy. In addition, users can [download entire databases](https://github.com/HajkD/biomartr/blob/master/vignettes/Database_Retrieval.Rmd) such as + +- `NCBI RefSeq` +- `NCBI nr` +- `NCBI nt` +- `NCBI Genbank` +- `ENSEMBL` +- `ENSEMBLGENOMES` + +with only one command. ### Citation @@ -51,7 +62,7 @@ The main difference between the [BiomaRt](http://www.bioconductor.org/packages/r Please consult the [Tutorials section](https://ropensci.github.io/biomartr/#tutorials) for more details. -`In the context of functional annotation retrieval` the `biomartr` package allows users to screen available marts using only the scientific name of an organism of interest instead of first searching for marts and datasets which support a particular organism of interest (which is required when using the `BiomaRt` package). Furthermore, `biomartr` allows you to search for particular topics when searching for attributes and filters. I am aware that the similar naming of the packages is unfortunate, but it arose due to historical reasons (please find a detailed explanation here: https://github.com/ropensci/biomartr/blob/master/FAQs.md and here #11). +`In the context of functional annotation retrieval` the `biomartr` package allows users to screen available marts using only the scientific name of an organism of interest instead of first searching for marts and datasets which support a particular organism of interest (which is required when using the `BiomaRt` package). Furthermore, `biomartr` allows you to search for particular topics when searching for attributes and filters. I am aware that the similar naming of the packages is unfortunate, but it arose due to historical reasons (please find a detailed explanation here: https://github.com/ropensci/biomartr/blob/master/FAQs.md and here [#11](https://github.com/ropensci/biomartr/issues/11)). I also dedicated [an entire vignette to compare](https://ropensci.github.io/biomartr/articles/Functional_Annotation.html) the `BiomaRt` and `biomartr` package functionality in the context of `Functional Annotation` (where their functionality overlaps which comprises about only 20% of the overall functionality of the biomartr package).