main.slnc

\slnc@note {marginpar}{6}{24699785}{En met Katsji en Puka ook, wanneer ze dat toelaten.}
\slnc@note {marginpar}{6}{20374409}{Yes Sai I stole this from you, shame- lessly.}
\slnc@note {marginpar}{7}{37282697}{Or, more accurately: dr. Strijbol, dr. Van Petegem, dr. Van den Camp and dr. Van der Jeugt}
\slnc@note {marginpar}{7}{21947273}{Or Lucifer and Lilith, our tiny demons}
\slnc@note {marginpar}{7}{19981193}{i carry your heart with me (i carry it in my heart) i am never without it}
\slnc@note {marginpar}{23}{12978664}{Maybe this should be more accurately called the ``Basic Assumption of Bio- logy'' \citep {cobb201760}.}
\slnc@note {marginpar}{29}{34136969}{Heteroscedastic: variance is not constant for all genes}
\slnc@note {marginpar}{111}{37675913}{R cannot represent row major dense matrices}
\slnc@note {marginpar}{111}{34923401}{You can pass either \lstinline {C} or \lstinline {F} on creation. This originates from C-style matrices (row-major) or Fortran-style matrices (column-major).}
\slnc@note {marginpar}{112}{24793993}{S3 is the oldest and simplest object-oriented class system in R. Other class systems in R are S4, reference classes, R6 and the proposed R7.}
\slnc@note {marginpar}{118}{12773894}{REPL: Read-Eval-Print Loop}
\slnc@note {marginpar}{123}{18406474}{Serialization is also commonly referred to as marshalling or pickling}
\slnc@note {marginpar}{174}{20767625}{What does down\-stream actually mean? The exploratory analysis is cyclical, each of the steps influencing each other.}
\slnc@note {marginpar}{174}{15655817}{This `double-dipping' dual use of data can lead to false-positive markers. \citep {denadel2025artificial,song2025synthetic}}
\slnc@note {marginpar}{178}{28799881}{At least for Zarr v3}
\slnc@note {marginpar}{179}{17417097}{The benchmark uses 13 different metrics, such as an Adjusted Rand Index or the overlap between highly variable genes before and after integration.}
\slnc@note {marginpar}{180}{32490377}{The PR fixing the issue has not been acknowledged yet by a maintainer. \texttt {\href {https://github.com/theislab/scgen/pull/104}{theislab/scgen\#104}}}
\slnc@note {marginpar}{185}{25954792}{We consider bioinformatics as an umbrella term, encompassing other research areas such as computational biology or systems biology.}
\slnc@note {marginpar}{186}{21554057}{Morphogenesis is the biological process causing cells or tissues to develop its shape.}
\slnc@note {marginpar}{186}{18408329}{The theory was eventually proven completely wrong.}
\slnc@note {marginpar}{187}{36103049}{This reminds of instrumentalism in science philosophy, positing that the value of a scientific theory lies only in how accurately it predicts observations and not how well it uncovers the unobserved aspects that explain these phenomena.}
\slnc@note {marginpar}{193}{30991241}{My PI personally reaching out seemed to be key; my mails remained unanswered.}
\slnc@note {marginpar}{195}{12305289}{Or as good as built-in, such as numpy matrices}
\slnc@note {marginpar}{197}{16536457}{This shift to Python is consistent with a general trend in software develop- ment: the 2024 stackoverflow survey and the 2024 state of the octo- verse indicated that Python is now the most widely used programming language.}