diff --git a/module-cheatsheets/RNA-seq-cheatsheet.md b/module-cheatsheets/RNA-seq-cheatsheet.md index 9861deab..7afdc63b 100644 --- a/module-cheatsheets/RNA-seq-cheatsheet.md +++ b/module-cheatsheets/RNA-seq-cheatsheet.md @@ -18,7 +18,9 @@ If you have a different version of R or other R packages, the documentation may - [`FastQC` and `fastp`](#fastqc-and-fastp) - [`ggplot2`](#ggplot2) - [`tximeta` and `SummarizedExperiment`](#tximeta-and-summarizedexperiment) -- [`stringr`, `readr`, `dplyr`, `pheatmap`](#stringr-readr-dplyr-pheatmap) +- [`stringr`, `readr`, `dplyr`](#stringr-readr-dplyr) +- [`ComplexHeatmap`](#complexheatmap) +- [`matrixStats`](#matrixstats) - [Salmon](#salmon) @@ -37,6 +39,7 @@ Read the [Base `R` package documentation](https://rdrr.io/r/). | Base `R` | [`all.equal()`](https://rdrr.io/r/base/all.equal.html) | All equal | Checks if two R objects are nearly equal | | Base `R` | [`attr()`](https://rdrr.io/r/base/attr.html) | Object Attributes | Gets or sets the attributes of an object | | Base `R` | [`rowSums()`](https://rdrr.io/r/base/colSums.html) | Row Sums | Returns the sum of the rows in a numeric matrix-like object (i.e.. a matrix, data.frame, etc.) | +| Base `R` | [`rowMeans()`](https://rdrr.io/r/base/colSums.html) | Row Means | Returns the mean of the rows in a number matrix-like object (i.e.. a matrix, data.frame, etc.) | | Base `R` | [`relevel()`](https://rdrr.io/r/stats/relevel.html) | Relevel | Reorders the levels of a factor as specified | | Base `R` | [`summary()`](https://rdrr.io/r/base/summary.html) | Object Summary | Returns a result summary of an object | | Base `R` | [`as.data.frame()`](https://rdrr.io/r/base/as.data.frame.html) | Data Frame | Checks if an object is a data.frame, and transforms the object into one, if possible | @@ -98,7 +101,7 @@ Read the [`SummarizedExperiment` package documentation (PDF)](http://bioconducto | `SummarizedExperiment`| [`assay()`; `assayNames()`](https://rdrr.io/bioc/SummarizedExperiment/man/SummarizedExperiment-class.html)| Assay or Assay Names| Accesses the assay data or the names of the assays from `SummarizedExperiment` object| -### `stringr`, `readr`, `dplyr`, `pheatmap` +### `stringr`, `readr`, `dplyr` Documentation for each of these packages can be accessed by clicking the package name in the table below. @@ -107,7 +110,25 @@ Documentation for each of these packages can be accessed by clicking the package | [`stringr`](https://stringr.tidyverse.org/index.html) |[`word()`](https://stringr.tidyverse.org/reference/word.html) | Word | Extracts words from a character vector | | [`readr`](https://readr.tidyverse.org/index.html) |[`write_rds()`](https://readr.tidyverse.org/reference/read_rds.html) | Write RDS | Writes data to a .RDS output file | | [`dplyr`](https://dplyr.tidyverse.org/) | [`pull()`](https://dplyr.tidyverse.org/reference/pull.html) | Pull | Extracts a variable (column) as a vector | -| [`pheatmap`](https://rdrr.io/cran/pheatmap/) | [`pheatmap()`](https://rdrr.io/cran/pheatmap/man/pheatmap.html) | Pretty heatmap | Plots clustered heatmaps | + +### `ComplexHeatmap` + +Read the [`ComplexHeatmap` Complete Reference](https://jokergoo.github.io/ComplexHeatmap-reference/book/). + +| Library/Package | Piece of Code | What it's called | What it does | +|-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| +| `ComplexHeatmap` | [`Heatmap()`](https://rdrr.io/bioc/ComplexHeatmap/man/Heatmap.html) | Heatmap constructor | Constructs a `Heatmap` class object that can then be used to plot a heatmap | +| `ComplexHeatmap` | [`HeatmapAnnotation()`](https://rdrr.io/bioc/ComplexHeatmap/man/HeatmapAnnotation.html) | Heatmap annotation constructor | Constructs a `HeatmapAnnotation` class object that can be used to annotate a heatmap | + +### `matrixStats` + +Read the [`matrixStats` package documentation (PDF)](https://cran.r-project.org/web/packages/matrixStats/matrixStats.pdf) and [summary of functions](https://cran.r-project.org/web/packages/matrixStats/vignettes/matrixStats-methods.html). + +| Library/Package | Piece of Code | What it's called | What it does | +|-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| +| `matrixStats` | [`rowVars()`](https://www.rdocumentation.org/packages/matrixStats/versions/1.3.0/topics/rowVars) | Row variance | Estimates the variance for each row in a matrix | +| `matrixStats` | [`rowSds()`](https://search.r-project.org/CRAN/refmans/matrixStats/html/rowSds.html) | Row standard deviations | Estimates the standard deviations for each row in a matrix | + ### Salmon diff --git a/module-cheatsheets/RNA-seq-cheatsheet.pdf b/module-cheatsheets/RNA-seq-cheatsheet.pdf index a8ca86e1..38081685 100644 Binary files a/module-cheatsheets/RNA-seq-cheatsheet.pdf and b/module-cheatsheets/RNA-seq-cheatsheet.pdf differ diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.md b/module-cheatsheets/pathway-analysis-cheatsheet.md index 56fd5d9e..47e7bdc7 100644 --- a/module-cheatsheets/pathway-analysis-cheatsheet.md +++ b/module-cheatsheets/pathway-analysis-cheatsheet.md @@ -16,7 +16,6 @@ If you have a different version of R or other R packages, the documentation may - [`msigdbr`](#msigdbr) - [AnnotationDbi](#annotationdbi) - [Base `R`](#base-r) -- [`DESeq2`](#deseq2) - [`enrichplot`](#enrichplot) - [`clusterProfiler`](#clusterprofiler) - [`GSVA`](#gsva) @@ -32,7 +31,7 @@ Read the [`msigdbr` documentation](https://rdrr.io/cran/msigdbr/f/README.md). | Library/Package| Piece of Code| What it's called| What it does | |----------------|--------------|-----------------|--------------| -| `msigdbr`| [`msigdbr()`](https://rdrr.io/cran/msigdbr/man/msigdbr.html)| TODO | Retrieves the specified MSigDB dataset | +| `msigdbr`| [`msigdbr()`](https://rdrr.io/cran/msigdbr/man/msigdbr.html)| Retrieve the MSigDB gene sets data frame | Retrieves the specified MSigDB dataset | ### AnnotationDbi @@ -50,9 +49,11 @@ Read the [Base `R` documentation](https://rdrr.io/r/). |Library/Package|Piece of Code|What it's called| What it does| |---------------|-------------|----------------|-------------| | Base `R`| [`fisher.test()`](https://rdrr.io/r/stats/fisher.test.html)| Fisher's Exact Test | Performs the Fisher's exact test for testing the null of independence of rows and columns for a given matrix or data.frame with count data | +| Base `R` | [`setdiff()`](https://rdrr.io/cran/probs/man/setdiff.html) | Set difference | Returns the difference of two sets (e.g., vectors) |
+ + ### `enrichplot` Read the [`enrichplot` package documentation (PDF)](https://bioconductor.org/packages/devel/bioc/manuals/enrichplot/man/enrichplot.pdf). @@ -91,7 +94,7 @@ Read the [`GSVA` package documentation](https://www.bioconductor.org/packages/re | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| | `GSVA` | [`gsva()`](https://rdrr.io/github/rcastelo/GSVA/man/gsva.html) | Gene Set Variation Analysis (GSVA) | Estimates gene set variation analysis enrichment scores on given gene expression matrix | -| `GSVA` | [`gsvaParam()`](https://rdrr.io/github/rcastelo/GSVA/man/gsvaParam-class.html) | Gene Set Variation Analysis (GSVA) | Specify parameters to use with `gsva()` | +| `GSVA` | [`gsvaParam()`](https://rdrr.io/github/rcastelo/GSVA/man/gsvaParam-class.html) | Gene Set Variation Analysis (GSVA) Parameters | Specify parameters to use with `gsva()` | ### `qusage` diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.pdf b/module-cheatsheets/pathway-analysis-cheatsheet.pdf index 9c49650d..6af2db1f 100644 Binary files a/module-cheatsheets/pathway-analysis-cheatsheet.pdf and b/module-cheatsheets/pathway-analysis-cheatsheet.pdf differ