UNDERSTAND

Who created this software? (Project, Organization, Person, Initiative, etc.)
Are there any additional contributors of note for this software ?
What useful features of this software are worth highlighting ?
[OPTIONAL] Who is the publisher of this software if not the author ?
[OPTIONAL] How can a user get support for the software ? (eg. Report bugs, request features and extensions, etc)
[OPTIONAL] Has the software been adopted in a project, organization or by a person?
[OPTIONAL] Is there any information about uses of this software (papers, research labs, etc) ?
[OPTIONAL] Are there any statistics of its use ?
[OPTIONAL] Are there any publications where the software is used ?
[OPTIONAL] Is there any benchmark information about the software ?
[OPTIONAL] What are the funding sources for this software?
[OPTIONAL] What are the ratings for this software?

What are domain specific keywords for this software ? (eg: hydrology, climate)
[OPTIONAL] Is there any other similar software that you know of ?
[OPTIONAL] What are the recommended uses and assumptions for the software ?
[OPTIONAL] Are there any constraints on use, situations it is not designed for, simplifications ?

EXECUTE

What is the URL for the code ?
- https://bioconductor.org/packages/release/bioc/html/customProDB.html
What license is the code released under ?
- Artistic-2.0
[OPTIONAL] Is there a URL for the executable ?

Is there any on-line documentation about the software ?
What language(s) is the software written in ?
What Operating Systems can the software run on ?
How can one install the software ?
What other software does the software require to be installed ?
[OPTIONAL] Are there estimates of how long it takes to run this software on average ?
[OPTIONAL] Are there any memory requirements for this software ?
[OPTIONAL] Are there any other important details about the implementation of this code (parallelization, special hardware, etc) ?

What input files does the software require ?
- - File Id:
    InputBAM
  - File Type:
    Mapped/Aligned BAM file produced by TopHat2/STAR like tools.
- - File Id:
    InputVCF
  - File Type:
    VCF (Variant Calling Format) file with variants/mutations identified by variant callers like MuTect, samtools.
- - File Id:
    InputBed
  - File Type:
    Splice junctions BED file produced by TopHat2/STAR like tools
- - File Id:
    InputFASTA
  - File Type:
    input human reference genome file.
What are the input parameters used for this software?
- novJunction: Similar to ii and iii. Looks for IDs from another Database. Specific to novel junctions.
What output files does the software produce ?
- - File Id:
    ProteinRPKMFasta
  - File Type:
    File with RPKM (quantitative information calculated). Sequences can be filtered based on an rpkm_cutoff
- - File Id:
    ProteinSNVFasta
  - File Type:
    Fasta File with proteomic sequences mutated due to SNVs (Single Nucleotide Variants) predicted by variant tools.
- - File Id:
    ProteinSNVTable
  - File Type:
    Table with all genomic variants and their protein mutation predictions.
- - File Id:
    ProteinIndelFasta
  - File Type:
    Fasta File with proteomic sequences mutated due to InDels (Insertions-Deletions) predicted by variant tools.
- - File Id:
  - File Type:
[OPTIONAL] Are there any relevant data catalogs that can be used with this software ?

What other software can interoperate with this one?
[OPTIONAL] Is this software typically used with other software in a workflow ? (eg: for visualization, preprocessing, postprocessing, etc)