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kescobo merged 3 commits into from
Jan 9, 2026
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Corrections/improvements to the current docs #18

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ae9ef65
corrections/improvements to the current docs
M-PERSIC Feb 12, 2025
62234ab
fix admonitions + other mistakes
M-PERSIC Feb 12, 2025
e87bc80
fix admonition + see -> consult
M-PERSIC Feb 12, 2025
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36 changes: 18 additions & 18 deletions docs/src/comparisons/bioconductor.md
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Expand Up @@ -9,15 +9,15 @@
* Packages cover a broard range of methods for the analysis and manipulation of
genomic data

**A few equivalent applications between BioJulia and Bioconductor:**
**A few similar applications between BioJulia and Bioconductor:**

| Application | BioJulia packages | Bioconductor packages |
|:--------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------|
| Data structures | [BioSymbols](https://biojulia.dev/BioSymbols.jl/stable/), [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl), [IntervalTrees](https://biojulia.dev/IntervalTrees.jl/stable/) | `Biobase` |
| Sequence annotation | [GenomicFeatures](https://biojulia.dev/GenomicFeatures.jl/stable/), [GenomicAnnotations](https://biojulia.dev/GenomicAnnotations.jl/dev/), [FormatSpecimens](https://github.com/BioJulia/FormatSpecimens.jl) | `AnnotationHub` |
| Input/Output | [FASTX](https://biojulia.dev/FASTX.jl/stable/), [XAM](https://biojulia.dev/XAM.jl/stable/), [BigWig](https://biojulia.dev/BigWig.jl/dev/),... | `BiocIO`, `Biostrings`, `ShortRead`,... |
| Sequence alignment | [BioSequences](https://biojulia.dev/BioSequences.jl/stable/), [BioAlignments](https://biojulia.dev/BioAlignments.jl/stable/) | `Biostrings` |
| Expression analysis | [SingleCellProjections](https://biojulia.dev/SingleCellProjections.jl/dev/) | `DESeq2` |
| Application | BioJulia packages | Bioconductor packages |
|:--------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------|
| Data structures | [BioSymbols](https://biojulia.dev/BioSymbols.jl/stable/), [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl), [IntervalTrees](https://biojulia.dev/IntervalTrees.jl/stable/) | `Biobase` |
| Sequence annotation | [GenomicFeatures](https://biojulia.dev/GenomicFeatures.jl/stable/), [GenomicAnnotations](https://biojulia.dev/GenomicAnnotations.jl/dev/), [FormatSpecimens](https://github.com/BioJulia/FormatSpecimens.jl) | `AnnotationHub` |
| Input/Output | [FASTX](https://biojulia.dev/FASTX.jl/stable/), [XAM](https://biojulia.dev/XAM.jl/stable/), [BigWig](https://biojulia.dev/BigWig.jl/dev/), etc. | `BiocIO`, `Biostrings`, `ShortRead`, etc. |
| Sequence alignment | [BioSequences](https://biojulia.dev/BioSequences.jl/stable/), [BioAlignments](https://biojulia.dev/BioAlignments.jl/stable/) | `Biostrings` |
| Expression analysis | [SingleCellProjections](https://biojulia.dev/SingleCellProjections.jl/dev/) | `DESeq2` |

**A few package/ecosystem equivalents between Julia and R:**

Expand All @@ -32,24 +32,24 @@

**A few notable differences between Julia and R:**

| Julia | R |
|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------|
| High-level, general-purpose compiled language | High-level, interpreted language for statistical computing |
| Dynamically typed with multiple dispatch and optional type annotations | Dynamically typed without type annotations support |
| Built-in parallelism via threads, coroutines (Tasks) | Parallelism via external libraries (BLAS, `parallel`,...) |
| Extensive metaprogramming (Lisp-like macros, generated functions,...) | Less extensive metaprogramming (function factories, expression manipulation,...) |
| Single implementation available (JuliaLang) | Multiple implementations available (pqR, Renjin,...) |
| Julia | R |
|:-----------------------------------------------------------------------|:----------------------------------------------------------------------------------|
| High-level, general-purpose compiled language | High-level, interpreted language for statistical computing and data visualization |
| Dynamically typed with multiple dispatch and optional type annotations | Dynamically typed without type annotations support |
| Built-in parallelism via threads, coroutines (Tasks) | Parallelism via external libraries (BLAS, `parallel`, etc.) |
| Lisp-like (homoiconic, macro-based) metaprogramming | Partially homoiconic, non-standard evaluation metaprogramming |
| Single implementation available (JuliaLang) | Multiple implementations available (pqR, Renjin, etc.) |

**To transition from R to Julia:**
* See [Noteworthy differences from
* Consult the [Noteworthy differences from
R](https://docs.julialang.org/en/v1/manual/noteworthy-differences/#Noteworthy-differences-from-R)
in the Julia manual for a more in-depth comparison
section in the Julia manual for a more in-depth comparison
* Use [RCall.jl](https://github.com/JuliaInterop/RCall.jl.git) to seamlessly
integrate R code into your Julia project
* Use
[JuliaCall](https://cran.r-project.org/web/packages/JuliaCall/readme/README.html)
to seamlessly integrate Julia code into your R project
* Check out the [Tidier.jl
ecosystem](https://tidierorg.github.io/Tidier.jl/dev/) for packages similar to
those commonly found in `tidyverse`
those commonly found in R's tidyverse

34 changes: 17 additions & 17 deletions docs/src/comparisons/biojava.md
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`org.biojava` package
* Launched in 2002 with six major releases covering more than 11 Java releases

**A few equivalent applications between BioJulia and BioJava:**
**A few similar applications between BioJulia and BioJava:**

| Application | BioJulia packages | BioJava modules |
|:--------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------|
| Input/Output | [FASTX](https://biojulia.dev/FASTX.jl/stable/), [XAM](https://biojulia.dev/XAM.jl/stable/), [BigWig](https://biojulia.dev/BigWig.jl/dev/),... | `nbio.genome.io.fastq`, `nbio.ontology.obo`,... |
| Sequence alignment | [BioSequences](https://biojulia.dev/BioSequences.jl/stable/), [BioAlignments](https://biojulia.dev/BioAlignments.jl/stable/) | `nbio.sequence`, `nbio.alignment` |
| Macromolecular structures | [BioStructures](https://biojulia.dev/BioStructures.jl/stable/) | `nbio.structure` |
| Application | BioJulia packages | BioJava modules |
|:--------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------|
| Input/Output | [FASTX](https://biojulia.dev/FASTX.jl/stable/), [XAM](https://biojulia.dev/XAM.jl/stable/), [BigWig](https://biojulia.dev/BigWig.jl/dev/), etc. | `nbio.genome.io.fastq`, `nbio.ontology.obo`, etc. |
| Sequence alignment | [BioSequences](https://biojulia.dev/BioSequences.jl/stable/), [BioAlignments](https://biojulia.dev/BioAlignments.jl/stable/) | `nbio.sequence`, `nbio.alignment` |
| Macromolecular structures | [BioStructures](https://biojulia.dev/BioStructures.jl/stable/) | `nbio.structure` |

**A few package/ecosystem equivalents between Julia and Java:**

Expand All @@ -28,20 +28,20 @@

**A few notable differences between Julia and Java:**

| Julia | Java |
|:-----------------------------------------------------------------------|:-----------------------------------------------------------------------------------------|
| High-level, general-purpose compiled language | High-level, object-oriented, two-step (compiled and interpreted) language |
| Expression-based (statements yield a value) | Statement-based (assignment as a statement) |
| Dynamically typed with multiple dispatch and optional type annotations | Statically typed with required type declarations |
| Built-in parallelism via threads, coroutines (Tasks) | Built-in parallelism via threads, streams, fibers (Project Loom) |
| Extensive metaprogramming (Lisp-like macros, homoiconicity,...) | Less extensive metaprogramming (reflection, annotations,...) |
| Included default package manager | No default package manager (dependency/build management tools include Maven, Gradle,...) |
| Single implementation available (JuliaLang) | Multiple implementations available (OpenJDK, GraalVM,...) |
| Julia | Java |
|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------|
| High-level, general-purpose compiled language | High-level, object-oriented, two-step (compiled and interpreted) language |
| Expression-based (statements yield a value) | Statement-based (statements don't always yield a value) |
| Dynamically typed with multiple dispatch and optional type annotations | Statically typed with required type declarations |
| Built-in parallelism via threads, coroutines (Tasks) | Built-in parallelism via threads, streams, fibers (Project Loom) |
| Lisp-like (homoiconic, macro-based) metaprogramming | Reflection-based runtime metaprogramming |
| Included default package manager | No default package manager (dependency/build management tools include Maven, Gradle, etc.) |
| Single implementation available (JuliaLang) | Multiple implementations available (OpenJDK, GraalVM, etc.) |

**To transition from Java to Julia:**
* Use [JavaCall.jl](https://juliainterop.github.io/JavaCall.jl/) to seamlessly
integrate Java code into your Julia project
* See [Running External
* Consult the [Running External
Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/)
in the Julia manual for running Java scripts or other programs from Julia
section in the Julia manual for running Java scripts or other programs from Julia

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