singularity-single-cell tagshttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags2024-03-20T21:20:05+01:00https://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.7v1.5.7- update rstudio-server and quarto
- added cellxgene-census and singler2024-03-20T21:20:05+01:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.6v1.5.6added cellxgene2024-02-28T18:09:14+01:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.5v1.5.5Fixed python installations. Added R package loupeR.2024-02-08T13:57:42+01:00Andreas Petzoldhttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.4v1.5.4- Updated RStudio and quarto
- Rewrote RStudio/conda integration
- Added authentication method for RStudio
- Updated to official Seurat v5 version
- Added R packages scuttle, SoupX, scDblFinder, sampleQC, harmony, lintr2024-01-25T09:01:07+01:00Andreas Petzoldhttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.3v1.5.3Added R packages gt and gtsummary.2023-10-18T21:06:10+02:00Andreas Petzoldhttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.2v1.5.2Added R packages styler and tictoc. Updated rstudio-server.2023-10-12T17:31:26+02:00Andreas Petzoldhttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.1v1.5.12023-10-10T13:11:34+02:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.5.0v1.5.0- Updated R to version 4.3
- Updated all R CRAN, Bioconductor and github packages to their most recent versions
- Switched to Seurat 5 for support of large datasets (using on-disk BPcells) and multimodal analyses (incl signac for scATAC-seq)
- Updated quarto
- Updated RStudio
- Added bedtools and samtools2023-08-15T18:17:53+02:00andpet0101andpet@gmx.dehttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.4.0v1.4.0- reproducibility of PCA is now tested
- cellrank v2 update
- several issues fixed2023-07-26T18:19:18+02:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.3.2v1.3.2built gdal library from source to fix compilation problems of depending r packages2023-05-05T18:31:24+02:00andpet0101andpet@gmx.dehttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.3.1v1.3.1added sccode, pydesq2, and pypath-omipath2023-04-24T19:58:46+02:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.3.0v1.3.0added scATAC packages Signac and SCENIC+
+some more fixes and tests<p data-sourcepos="1:1-1:101" dir="auto"><code>singularity shell oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.3.0</code></p>
<ul data-sourcepos="3:1-5:40" dir="auto">
<li data-sourcepos="3:1-3:46">fixed issue with RStudio Server not starting</li>
<li data-sourcepos="4:1-4:54">added tests for RStudio Server and Jupyter Lab start</li>
<li data-sourcepos="5:1-5:40">added scATAC packages Signac & SCENIC+</li>
</ul>2023-04-05T11:03:39+02:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.2.2v1.2.2<p data-sourcepos="1:1-1:99" dir="auto">singularity shell <a href="oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.2.2">oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.2.2</a></p>2023-02-03T16:35:18+01:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.2.1v1.2.1- fixed cellrank<p data-sourcepos="1:1-1:101" dir="auto"><code>singularity shell oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.2.1</code></p>
<ul data-sourcepos="3:1-3:16" dir="auto">
<li data-sourcepos="3:1-3:16">fixed cellrank</li>
</ul>2023-01-13T15:38:28+01:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.2.0v1.2.0update R and python packages<ul data-sourcepos="1:1-7:83" dir="auto">
<li data-sourcepos="1:1-2:0">
<p data-sourcepos="1:3-1:103"><code>singularity shell oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.2.0</code></p>
</li>
<li data-sourcepos="3:1-4:0">
<p data-sourcepos="3:3-3:91">up-to-date R and python packages, the newest version of RStudio and quarto for publishing</p>
</li>
<li data-sourcepos="5:1-7:83">
<p data-sourcepos="5:3-5:138">since RStudio needs to write some runtime information and the container is read-only, you will need to mount two additional directories:</p>
<ul data-sourcepos="7:3-7:83">
<li data-sourcepos="7:3-7:83"><code>-B <some_path>:/var/run/rstudio-server -B <some_path>:/var/lib/rstudio-server</code></li>
</ul>
</li>
</ul>2023-01-13T13:20:06+01:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.1.0v1.1.0added liana for cell-cell communication<p data-sourcepos="1:1-1:99" dir="auto">singularity shell <a href="oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.1.0">oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.1.0</a></p>2022-10-05T14:56:41+02:00Fabian Rosthttps://gitlab.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell/-/tags/v1.0.0v1.0.0<p data-sourcepos="1:1-1:99" dir="auto">singularity shell <a href="oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.0.0">oras://gcr.hrz.tu-chemnitz.de/dcgc-bfx/singularity/singularity-single-cell:v1.0.0</a></p>2022-08-25T22:26:59+02:00Fabian Rost