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NEWS.Rmd
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---
output: github_document
---
# Giotto 1.0.1 - 1.0.3
- Fixed bugs
- Added seed to HMRF
- Created functions to read 10X Visium .h5 files
- see **createGiottoVisiumObject** to create a Giotto object directly
- see **get10Xmatrix_h5** to extract the count matrix
# Giotto 1.0.0
This is the first major release of Giotto. If you still want to work with the previous version,
then you can find the older releases [here](https://github.com/RubD/Giotto/tags).
Here is an overview about what has changed in the meantime:
- **NEW:** Addition of **getSpatialDataset** to directly download a spatial dataset
(expression matrix, spatial coordinates and metadata). This is now also included in the
examples that you can find under the **Datasets** tab on this website.
- **NEW:** We have added tools to install, remove and check a Giotto r-miniconda environment.
This miniconda environment is one way to make sure that you can run functions that require Python modules.
- **installGiottoEnvironment**: (re-)installs a Giotto miniconda environment
- **removeGiottoEnvironment**: removes a Giotto miniconda environment
- **checkGiottoEnvironment**: verifies if a Giotto environment can be found
The other alternative is to [install](https://rubd.github.io/Giotto_site/articles/installation_issues.html#python-manual-installation) them in your own favorite Python environment and
provide the path in the **createGiottoInstructions** command.
- extension and improvement of spatial gene detection methods:
- **NEW:** addition of **spark** method
- improvements for silhouetteRank:
- faster implementation
- multi parameter version as **silhouetteRankTest**
- improvements for binSpect:
- faster implementation
- multi parameter version: **binSpectSingle** or **binSpectMulti**
- Spatial cell type enrichment methods have been streamlined and updated
- **runPAGEEnrich** to run enrichment using PAGE algorithm and selected marker genes
- **runRankEnrich** to run enrichment using a whole expression matrix
- **runHyperGeometricEnrich** to run enrichment using the hypergeometric test
- **NEW:** Spatial cell type deconvolution has been added:
- use **runSpatialDeconv** or **runDWLSDeconv**
- **NEW:** Addition of **addCellIntMetadata** to add information about interacting cell types,
which can subsequently be viewed with the spatPlot commands.
- **NEW:** Addition of 3 small vignettes that cover different types of spatial datasets:
- single-cell resolution ([mini seqFISH+](../articles/mini_seqfish.html))
- multi-cell resolution ([mini visium](../articles/mini_visium.html))
- 3D dataset ([mini STARmap](../articles/mini_starmap.html))
- See **data(package = 'Giotto')**
- Cell Proximity Genes has been changed to Interaction Changed Genes
- This better reflects the nature of gene changes due to neighboring cell interactions
- CPG functions are deprecated and will be removed in the future
- Several function help pages have been updated with dummy example code
- several small and big fixes to the code
# Giotto 0.3.5
- background images See [howto's](../articles/howto_images.html)
- support for sparse matrices
- PCA can be calculated with the packages irlba (default) or factominer (old default)
- complemented PCA with separate functions for a scree plot and jackstraw plot
- addition of **readExprMatrix** to read an expression matrix
- addition of **addGenesPerc** to add information about genesets (e.g. mitochondrial genes)
- addition of **showGrids** and **showNetworks** to see available spatial grids and networks
- several bug fixes
# Giotto 0.3.2
- added voronoi plots to use in spatial plotting. See [howto's](../articles/howto_voronoi_plots.html)
- generalized visualization parameters between functions
# Giotto 0.3.1
- (optional) automatic installation of python modules through reticulate:
- you can provide your preferred python path
- the giotto environment can be installed automatic
- if you do not provide the python path and do not choose to install the giotto environment, then it will take the default python path
- several bug fixes
- several mini-datasets are now included within Giotto for quick testing:
- field 1 of seqFISH+ (single-cell)
- the visium brain Dentate Gyrus subset (spots)
- subset of starMAP (3D)
example to acces the seqFISH+ mini dataset:
```{r, eval=FALSE}
# raw counts
small_seqfish_expr_matrix = read.table(system.file("extdata", "seqfish_field_expr.txt", package = 'Giotto'))
# cell locations
small_seqfish_locations = read.table(system.file("extdata", "seqfish_field_locs.txt", package = 'Giotto'))
```
# Giotto 0.3.0
- Default spatial network created with **createSpatialNetwork** is now a Delaunay spatial network.
```{r, eval=FALSE}
# to create the old default kNN spatial network use:
createSpatialKNNnetwork(gobject)
# or use this function with the following setting
createSpatialNetwork(gobject, method = 'kNN')
```
- The function names for extracting spatial genes have changed:
```{r, eval=FALSE}
# binGetSpatialGenes is now:
binSpect(gobject) # binary Spatial extraction
# spatial_genes_python is now:
silhouetteRank(gobject)
```
- Fixed multiple bugs
- Improved speed by changing code to Rcpp and implementing parallelization options
- updated [howto's](../articles/getting_started.html) tutorials in Start section
- Finished the analysis of 10 different spatial datasets (tutorials are a work-in-progress)
# Giotto 0.2.4
- New examples on mouse kidney and brain using the recently released [10X Visium datasets](https://www.10xgenomics.com/spatial-transcriptomics/) (**NEW**)
- Added tools to identify spatial enrichment based on cell-type specific gene signature lists (**NEW**)
# Giotto 0.2.3
- New example with 3D-like spatial data of the mouse hypothalamic preoptic region using [merFISH](https://science.sciencemag.org/content/362/6416/eaau5324) (**NEW**)
- New example with 3D spatial data [STARmap](https://science.sciencemag.org/content/361/6400/eaat5691)
- New example with the highly sensitive data from [osmFISH](https://www.nature.com/articles/s41592-018-0175-z)
- New example on the Cerebellum with the scalable data from [Slideseq](https://science.sciencemag.org/content/363/6434/1463)
- New example on mouse olfactory bulb using immobilized primers on glass slides from [Spatial Transcriptomics](https://science.sciencemag.org/content/353/6294/78)
- Updated seqFISH+ cortex example (**NEW**)
- Updated STARmap cortex example (**NEW**)
# Giotto 0.2.2
- Implemented [SpatialDE](https://github.com/Teichlab/SpatialDE) and [trendsceek](https://github.com/edsgard/trendsceek)
- Updated support for 3D spatial data
- Added support for the use of global instructions and automatically saving your plots (**NEW**)
- Add wrapper for differential expression with [MAST](https://github.com/RGLab/MAST) and [SCRAN](https://bioconductor.org/packages/release/bioc/html/scran.html)