I could not agree with you more. It is a disconcerting trend to see high impact papers using an "in house program" or "a modified version of a previously descr

I could not agree with you more. It is a disconcerting trend to see high impact papers using an "in house program" or "a modified version of a previously described tool", without providing any details about software versions, analysis steps and any custom filtering applied to the data. There could be bugs, unintentionally (or intentionally) introduced biases, or other things such as outlier removal that are not explained in the manuscripts methods. This is also very true for statistical analysis, many papers do not provide R scripts for their analysis and only a brief overview of the analysis.