This is the repository: https://github.com/Vivianstats/scImpute
*Ana Carolina Leote* *MSc. Biological Engineering* *PhD student at the Cologne Graduate School for Ageing Research* *Cellular networks and systems biology (Beyer group), **CECAD Research Center* https://www.linkedin.com/in/anacarolinaleote/ On Wed, Feb 10, 2021 at 6:44 PM Vincent Carey <st...@channing.harvard.edu> wrote: > It is wise to be careful here. If we don't know the provenance of the > code in github it might actually be someone else's. > It reminds me of the Numerical Recipes events, in which folks > redistributed proprietary code without permission. > What repo are we talking about anyway? > > On Wed, Feb 10, 2021 at 12:38 PM Martin Morgan <mtmorgan.b...@gmail.com> > wrote: > >> I don’t know what the legal requirement is. >> >> As a human if I hadn’t given explicit consent I’d like to be asked. And >> if I had used someone else’s code I’d like it to be transparent that my use >> was legitimate, and a private exchange of email between me and the other >> individual consenting to use their code wouldn’t be transparent enough. >> Hopefully I’m not being hypocritical here. >> >> Martin >> >> From: Ana Carolina Leote <anacarolinale...@gmail.com> >> Date: Wednesday, February 10, 2021 at 10:24 AM >> To: "Kern, Lori" <lori.sheph...@roswellpark.org> >> Cc: Martin Morgan <mtmorgan.b...@gmail.com>, Wolfgang Huber < >> wolfgang.hu...@embl.org>, "bioc-devel@r-project.org" < >> bioc-devel@r-project.org> >> Subject: Re: [Bioc-devel] How to integrate code from a package not >> available on bioconductor >> >> My motivation to include this package is that my own package includes, >> but is not limited to, an ensemble of different packages that attempt to >> solve the same problem, besides my own solution, since I did some work >> showing they all have their pros and cons. At the moment my package does >> not include this one, because of all the problems here raised, but since it >> is arguably more popular than all other "alternative" packages, I felt I >> should include it. This is why using an alternative package unfortunately >> does not solve my problem. I also looked in the page Lori shared but this >> package is not there. However you do raise very valid points. I think I >> need to weigh the cost of changing the code against the additional >> usefulness my package can gain more carefully than I did so far. >> >> I do have one additional question, though. Martin mentioned the license >> compatibility. There is no license at all in the GitHub repository of this >> package. I did some searching but I'm not sure what the default GitHub >> copyright means for bioconductor distribution. Does it mean I am not >> allowed to include this code in case I do wish to go forward with taking >> the code "as is"? >> >> Thanks again for all your helpful responses. It's great as a new >> developer to have such support. >> >> Best, >> Carolina >> >> Ana Carolina Leote >> MSc. Biological Engineering >> PhD student at the Cologne Graduate School for Ageing Research >> Cellular networks and systems biology (Beyer group), CECAD Research Center >> https://www.linkedin.com/in/anacarolinaleote/ >> >> >> On Wed, Feb 10, 2021 at 3:50 PM Kern, Lori <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>> wrote: >> Have you looked at some of the scRNA packages that are already on >> Bioconductor to see if there is similar functionality in an existing >> package already accepted? >> You can search for packages that have scRNA in the package name or title >> on this page: >> http://bioconductor.org/packages/release/BiocViews.html#___Software >> >> depending there is also a single cell workflow that might point to >> similar functionality >> >> http://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html >> >> >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Comprehensive Cancer Center >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> >> ________________________________ >> From: Bioc-devel <bioc-devel-boun...@r-project.org<mailto: >> bioc-devel-boun...@r-project.org>> on behalf of Martin Morgan < >> mtmorgan.b...@gmail.com<mailto:mtmorgan.b...@gmail.com>> >> Sent: Wednesday, February 10, 2021 9:36 AM >> To: Ana Carolina Leote <anacarolinale...@gmail.com<mailto: >> anacarolinale...@gmail.com>>; Wolfgang Huber <wolfgang.hu...@embl.org >> <mailto:wolfgang.hu...@embl.org>> >> Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> < >> bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> >> Subject: Re: [Bioc-devel] How to integrate code from a package not >> available on bioconductor >> >> If the package is already widely used, then I guess it provides useful >> functionality, and so your package doesn't have to provide that >> functionality, so perhaps a better solution is to refer users to the >> unsupported package in your vignette?? >> >> What you say about not being maintained in over a year is probably the >> main concern with using code that is not in CRAN or Bioconductor. Already >> the code could be buggy, not well tested, and poorly documented (even if >> widely used! and of course the code / documentation could be excellent...) >> because it has not been subject to regular R CMD check etc or to initial >> review. And now the original author of the code is not maintaining it, so >> *you* have to fully understand it so that you can address bugs etc. As a >> 'developer' this could be my worst nightmare -- having to spend my time >> cursing at code somebody else wrote, instead of cursing at my own code! >> >> The license of the package needs to permit use of the code, or may >> restrict how your own code is used (e.g., if the package is licensed for >> 'academic use only' then likely your package would need to be licensed >> similarly, and then would not be appropriate for Bioconductor). >> >> All of these would discourage me from adopting this code. >> >> Martin >> >> On 2/10/21, 9:11 AM, "Bioc-devel on behalf of Ana Carolina Leote" < >> bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org> >> on behalf of anacarolinale...@gmail.com<mailto:anacarolinale...@gmail.com>> >> wrote: >> >> Dear all, >> Thank you so much for the great input and to Wolfgang for raising >> these >> points. >> I am afraid I gain more than I lose by including this particular >> package, >> as it is somewhat commonly used in the scRNA-seq community. It seems >> not to >> be maintained in over a year, however, judging by the dates of the >> latest >> response to issues and commits on GitHub. For this reason I think the >> probability of it being updated is low, so I was planning to take the >> code >> "as is" and assume maintainership - this after contacting the authors >> as >> suggested. >> >> Thanks and best wishes, >> Carolina >> >> *Ana Carolina Leote* >> *MSc. Biological Engineering* >> *PhD student at the Cologne Graduate School for Ageing Research* >> *Cellular networks and systems biology (Beyer group), **CECAD Research >> Center* >> >> https://secure-web.cisco.com/1JCGueviBWl7DVrqkMofRc1S6sTjcVSsAg_KFX33Rpki72itBTsrUNlyADxYZ8tuocj7u69YtSf-7bFFmVOQMd1LvSaQzIL3jICkqmRGElXvH6G1o3ApsV6GOaWTR_XtENn8RxRS3QttiyUulE0H01k-_iWcOhrzOp-LHAeNI07GwXycEjob0NEObtaQ7SpF5MCbuDjEVhJyY2_-nmtHPv-WC5Z8PNo0Ua3teNqOKv2ki1VriQI-M9WQVuOr2S28BGuI69w0aQMQmbHz1wuNxeuWxqdYybR1_49yIN2ZLjcikEyXy-RetsPZByGvHX1_i/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F >> >> >> On Wed, Feb 10, 2021 at 2:51 PM Wolfgang Huber < >> wolfgang.hu...@embl.org<mailto:wolfgang.hu...@embl.org>> >> wrote: >> >> > >> > >> > > Il giorno 10feb2021, alle ore 14:31, Kern, Lori >> > <lori.sheph...@roswellpark.org> ha scritto: >> > > >> > > Have you reached out to the maintainer of the github package to >> see if >> > they would plan on submitting to CRAN or Bioconductor? >> > > If they do not, you could see if they are okay with you >> including the >> > code in your package and then clearly indicate their authorship in >> the man >> > pages and by giving contributor credit in the DESCRIPTION. They >> might also >> > include CITATION information in their package to include? >> > > >> > > Others might have additional thoughts? >> > >> > Ana, >> > >> > if you are in a position to take that other code “as is” and then >> assume >> > maintainership over it, this may be a way forward. However, >> consider these >> > issues in advance: >> > - What happens if these other authors change their code on GitHub? >> Will >> > you also synchronize the copy in your own package, or leave it as >> is? This >> > requires a process and potentially continuous resources. >> > - Who is responsible for fixing bugs in that copied code? >> > - There are many reasons why people might not put their code on >> CRAN and >> > Bioconductor, but in case it is a sign of low confidence in the >> quality of >> > the code or low commitment to maintain it, depending on it incurs >> > additional technical debt for you. >> > >> > Are there maybe other packages (on CRAN/Bioconductor) that provide >> what >> > you need? >> > >> > Kind regards >> > Wolfgang >> > >> > >> > > >> > > Cheers, >> > > >> > > >> > > Lori Shepherd >> > > >> > > Bioconductor Core Team >> > > >> > > Roswell Park Comprehensive Cancer Center >> > > >> > > Department of Biostatistics & Bioinformatics >> > > >> > > Elm & Carlton Streets >> > > >> > > Buffalo, New York 14263 >> > > >> > > ________________________________ >> > > From: Bioc-devel <bioc-devel-boun...@r-project.org<mailto: >> bioc-devel-boun...@r-project.org>> on behalf of Ana >> > Carolina Leote <anacarolinale...@gmail.com<mailto: >> anacarolinale...@gmail.com>> >> > > Sent: Wednesday, February 10, 2021 5:14 AM >> > > To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> < >> bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> >> > > Subject: [Bioc-devel] How to integrate code from a package not >> available >> > on bioconductor >> > > >> > > Dear all, >> > > >> > > I am a package maintainer and would like to add a functionality >> that >> > > depends on another package which is not available in >> bioconductor, only >> > via >> > > GitHub. I would like to make the necessary changes in order to be >> able to >> > > use their code in my package. Can anyone point me towards the >> best way to >> > > proceed without undermining the authorship of the original >> developers? Is >> > > copying their code to my package and editing it to bioconductor >> standards >> > > appropriate? >> > > >> > > Thank you and best wishes, >> > > Carolina >> > > >> > > *Ana Carolina Leote* >> > > *MSc. Biological Engineering* >> > > *PhD student at the Cologne Graduate School for Ageing Research* >> > > *Cellular networks and systems biology (Beyer group), **CECAD >> Research >> > > Center* >> > > >> > >> https://secure-web.cisco.com/1sN_yjFZ4rXsNHMf8Fp8CJTySgKw-1exyK2uoJVgve2HB-ffaKVZpjVqnqKkiHfvj-8XfBD5L-E-u5CSB1GVD7eouovHeu4HCMh60N2H2o2WA8SOPodHnGfUgo8J3fWYeoSrQCiNJ5M4yE2VTnUi-WGlGdJeBDFxKTQwTFVThCjoTyAwk1tTdVAznZxVTGkCNBmBuV1Na-a0-81QaIYra4grO9-57FesPlxZIA0WUU9icoS3LgqlPTUhsmLZUM0NmejCSrTNSDA9AzDs7tB66TW4lBTvaNpOHMrk5wPCYIPckLqpDkVL3HnRSiWmXdWJE/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fanacarolinaleote%2F >> > > >> > > [[alternative HTML version deleted]] >> > > >> > > _______________________________________________ >> > > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> >> mailing list >> > > >> > >> https://secure-web.cisco.com/1vxzYOt1Hk0jYyShxe8B714l2GGAvh6Qvfo2Ey_49Ro47iSw83aMqNIB5Qv3keiqGApswE2x6TuWzoZjp-NJuEJcrt-skDYLR1Lsd0m1gCdOno-5vOXu1DHnuKsRkZQEyXRX00TjWpnBjbIwuJq5ll1xYmpurSpXNAagbyUQpcfZ136DgLhfGEM63BY-2KzMOwYsXqzpFhqcGhYhR1BkRDJBlIK7NjrhbsQ_8f4Hn2n7yvll4i20POhhaeiLBMZwwu0HXiWtT8v6VNA8pbxf7YxHpISCef2JJErtEjx21uA1ZQxeTNYg3X_37zZDJYGcZ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel >> > > >> > > >> > > >> > > This email message may contain legally privileged and/or >> confidential >> > information. 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