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I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package.

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in what format do you want the pathways? You can bulk download the SBML files. Also, please clarify what you mean by "download the genes of each pathway". – WYSIWYG Apr 21 '14 at 9:22
What pathways? From which database? What species? – terdon Apr 21 '14 at 10:58
up vote 1 down vote accepted

Try using KEGG REST. ## list of all genes and pathways in Humans

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Do you mind showing me how you got this file? – user258682 May 4 '14 at 17:03
You can find it in the rest page. – Prakki Rama May 9 '14 at 6:42

If you're working with BioCyc pathways you can use their REST-API for batch-downloading all genes for their pathways. You can run a wide range of queries including BioVelo-queries for all genes/compounds in a specified pathway, all pathways in organism etc. A query for all the pathways in B. subtilis would look like:[x:x%3C-bsub^^pathways]

Where you get an XML with the Cyc-IDs for the pathways which can be used to search for the genes. A query for all genes in the Arginine synthesis pathway in B. subtilis would then look like:[x:y:=bsub~argsyn-pwy,x%3C-%28genes-of-pathway%20y%29]&detail=full

Which returns an XML with information regarding the genes, start and end positions including (i.e. gene length). Since I don't work very much in R I don't know if there exists an R-package. But it is very straightforward to write Python scripts for downloading and XML-parsing.

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