diff --git a/module-cheatsheets/RNA-seq-cheatsheet.md b/module-cheatsheets/RNA-seq-cheatsheet.md index 64c114c9..9861deab 100644 --- a/module-cheatsheets/RNA-seq-cheatsheet.md +++ b/module-cheatsheets/RNA-seq-cheatsheet.md @@ -5,76 +5,97 @@ > Please note that these tables are not intended to tell you all the information you need to know about each command. > > The hyperlinks found in each piece of code will take you to the documentation for further information on the usage of each command. +Please be aware that the documentation will generally provide information about the given function's most current version (or a recent version, depending on how often the documentation site is updated). +This will usually (but not always!) match what you have installed on your machine. +If you have a different version of R or other R packages, the documentation may differ from what you have installed. + + + +**Table of Contents** + +- [Base `R`](#base-r) +- [`DESeq2`](#deseq2) +- [`FastQC` and `fastp`](#fastqc-and-fastp) +- [`ggplot2`](#ggplot2) +- [`tximeta` and `SummarizedExperiment`](#tximeta-and-summarizedexperiment) +- [`stringr`, `readr`, `dplyr`, `pheatmap`](#stringr-readr-dplyr-pheatmap) +- [Salmon](#salmon) + +
### Base `R` -Read the Base `R` package documentation [**here**](https://www.rdocumentation.org/packages/base/versions/3.5.1). + +Read the [Base `R` package documentation](https://rdrr.io/r/). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| Base `R` | [`list.files()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/list.files) | List files | Produces a character vector of files or directories in the specified directory | -| Base `R` | [`names()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/names) | Names | Gets or sets the names of an object | -| Base `R` | [`colnames()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/row%2Bcolnames) | Column names | Gets or sets the column names of a matrix or data frame | -| Base `R` | [`all.equal()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/all.equal) | All equal | Checks if two R objects are nearly equal | -| Base `R` | [`attr()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/attr) | Object Attributes | Gets or sets the attributes of an object | -| Base `R` | [`rowSums()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/colSums) | Row Sums | Returns the sum of the rows in a numeric matrix-like object (i.e.. a matrix, data.frame, etc.) | -| Base `R` | [`relevel()`](https://www.rdocumentation.org/packages/stats/versions/3.5.1/topics/relevel) | Relevel | Reorders the levels of a factor as specified | -| Base `R` | [`summary()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/summary) | Object Summary | Returns a result summary of an object | -| Base `R` | [`as.data.frame()`](https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/as.data.frame) | Data Frame | Checks if an object is a data.frame, and transforms the object into one, if possible | +| Base `R` | [`list.files()`](https://rdrr.io/r/base/list.files.html) | List files | Produces a character vector of files or directories in the specified directory | +| Base `R` | [`names()`](https://rdrr.io/r/base/names.html) | Names | Gets or sets the names of an object | +| Base `R` | [`colnames()`](https://rdrr.io/r/base/colnames.html) | Column names | Gets or sets the column names of a matrix or data frame | +| 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` | [`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 | ### `DESeq2` -Read the `DESeq2` package documentation [**here**](https://bioc.ism.ac.jp/packages/3.8/bioc/manuals/DESeq2/man/DESeq2.pdf), and the package vignette by Love, Anders, and Huber [**here**](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html). + +Read the [`DESeq2` package documentation (PDF)](https://www.bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf), and the [package vignette by Love, Anders, and Huber](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| `DESeq2` | [`vst()`](https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/vst) | Variance Stabilizing Transformation | Applies variance stabilizing transformation to data (log2-like scale) | -| `DESeq2` | [`DESeqDataSet()`](https://www.rdocumentation.org/packages/DESeq/versions/1.24.0/topics/DESeqDataSet-class)| DESeqDataSet constructor that can take a `SummarizedExperiment`| Creates a DESeqDataSet object | -| `DESeq2` | [`DESeqDataSetFromMatrix()`](https://www.rdocumentation.org/packages/DESeq/versions/1.24.0/topics/DESeqDataSet-class)| DESeqDataSet constructor | Creates a DESeqDataSet object from a matrix of count data | -| `DESeq2` | [`DESeq()`](https://www.rdocumentation.org/packages/DESeq/versions/1.24.0/topics/DESeq) | Differential Expression Analysis Based on the Negative Binomial Distribution | Estimates size factors, estimates dispersion, and performs negative binomial fitting and Wald statistics as steps in the default DESeq2 differential expression analysis | -| `DESeq2` | [`plotPCA()`](https://www.rdocumentation.org/packages/DESeq/versions/1.24.0/topics/plotPCA) | PCA plot | Produces a principal component analysis plot for transformed data. It can be used to visually inspect the data, which might allow an analyst to identify batch effects. | -| `DESeq2` | [`counts()`](https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/counts) | Counts | Returns count matrix from `DESeqDataSet` object | -| `DESeq2` | [`results()`](https://www.rdocumentation.org/packages/DESeq/versions/1.24.0/topics/results) | Results | Returns the results table from a DESeq2 analysis | -| `DESeq2` | [`assay()`](https://www.bioconductor.org/packages/devel/bioc/manuals/DESeq2/man/DESeq2.pdf) | Assay | Returns matrix from the `assay` slot of a `DESeqDataSet` object | +| `DESeq2` | [`vst()`](https://rdrr.io/bioc/DESeq2/man/vst.html) | Variance Stabilizing Transformation | Applies variance stabilizing transformation to data (log2-like scale) | +| `DESeq2` | [`DESeqDataSet()`](https://rdrr.io/bioc/DESeq2/man/DESeqDataSet.html)| DESeqDataSet constructor that can take a `SummarizedExperiment`| Creates a DESeqDataSet object | +| `DESeq2` | [`DESeqDataSetFromMatrix()`](https://rdrr.io/bioc/DESeq2/man/DESeqDataSet.html)| DESeqDataSet constructor | Creates a DESeqDataSet object from a matrix of count data | +| `DESeq2` | [`DESeq()`](https://rdrr.io/bioc/DESeq2/man/DESeq.html) | Differential Expression Analysis Based on the Negative Binomial Distribution | Estimates size factors, estimates dispersion, and performs negative binomial fitting and Wald statistics as steps in the default DESeq2 differential expression analysis | +| `DESeq2` | [`plotPCA()`](https://rdrr.io/bioc/DESeq2/man/plotPCA.html) | PCA plot | Produces a principal component analysis plot for transformed data. It can be used to visually inspect the data, which might allow an analyst to identify batch effects. | +| `DESeq2` | [`counts()`](https://rdrr.io/bioc/DESeq2/man/counts.html) | Counts | Returns count matrix from `DESeqDataSet` object | +| `DESeq2` | [`results()`](https://rdrr.io/bioc/DESeq2/man/results.html) | Results | Returns the results table from a DESeq2 analysis | +| `DESeq2` | [`assay()`](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#extracting-transformed-values) | Assay | Returns matrix from the `assay` slot of a `DESeqDataSet` object | ### `FastQC` and `fastp` -Read the `FastQC` documentation [**here**](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the `fastp` documentation [**here**](https://github.com/OpenGene/fastp). +Read the [`FastQC` documentation](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the [`fastp` documentation](https://github.com/OpenGene/fastp). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| | `fastp` | [`fastp`](https://github.com/OpenGene/fastp) | FASTQ preprocessor | Preprocesses FASTQ files through adapter trimming, quality filtering, length filtering, and a number of additional options | -| `FastQC` | [`fastqc`](https://www.rdocumentation.org/packages/fastqcr/versions/0.1.2/topics/fastqc) | FASTQC (Quality Control) | Performs quality control checks on raw sequence data and outputs a QC(quality control) report | +| `FastQC` | [`fastqc`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | FASTQC (Quality Control) | Performs quality control checks on raw sequence data and outputs a QC (quality control) report | ### `ggplot2` -Read the `ggplot2` package documentation [**here**](https://www.rdocumentation.org/packages/ggplot2/versions/3.1.0). A vignette on the usage of the `ggplot2` package can be found [**here**](https://cran.r-project.org/web/packages/ggplot2/vignettes/ggplot2-specs.html). +Read the [`ggplot2` package documentation](https://ggplot2.tidyverse.org/), an [overall reference for `ggplot2` functions](https://ggplot2.tidyverse.org/reference/index.html), and a [vignette on the usage of the `ggplot2` aesthetics](https://ggplot2.tidyverse.org/articles/ggplot2-specs.html). +Additional vignettes are available from the "Articles" dropdown menu on this webpage. | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| `ggplot2` | [`ggsave()`](https://www.rdocumentation.org/packages/ggplot2/versions/3.1.0/topics/ggsave) | GG Save | Saves the last plot in working directory | -| `ggplot2` | [`last_plot()`](https://www.rdocumentation.org/packages/ggplot2/versions/3.1.0/topics/last_plot) | Last plot | Returns the last plot produced | -| `ggplot2` | [`geom_point()`](https://www.rdocumentation.org/packages/ggplot2/versions/3.1.0/topics/geom_point) | Geom point | Creates a scatterplot (when added to the `ggplot()` function) | -| `ggplot2` | [`xlab()`; `ylab()`](https://www.rdocumentation.org/packages/ggplot2/versions/3.1.0/topics/labs) | X Axis Labels; Y Axis Labels | Modifies the labels on the x axis and on the y axis, respectively | -| `ggplot2` | [`coord_fixed()`](https://www.rdocumentation.org/packages/ggplot2/versions/3.1.0/topics/coord_fixed) | Cartesian Coordinates with Fixed Aspect Ratio | Coerces the coordinates on the plot to represent a fixed specified ratio | +| `ggplot2` | [`ggsave()`](https://ggplot2.tidyverse.org/reference/ggsave.html) | GG Save | Saves the last plot in working directory | +| `ggplot2` | [`last_plot()`](https://ggplot2.tidyverse.org/reference/last_plot.html) | Last plot | Returns the last plot produced | +| `ggplot2` | [`geom_point()`](https://ggplot2.tidyverse.org/reference/geom_point.html) | Geom point | Creates a scatterplot (when added to the `ggplot()` function) | +| `ggplot2` | [`labs()`; `xlab()`; `ylab()`](https://ggplot2.tidyverse.org/reference/labs.html) | X Axis Labels; Y Axis Labels | Modifies the plot labels, with specific functions for the x axis and y axis, respectively | +| `ggplot2` | [`coord_fixed()`](https://ggplot2.tidyverse.org/reference/coord_fixed.html) | Cartesian Coordinates with Fixed Aspect Ratio | Coerces the coordinates on the plot to represent a fixed specified ratio | ### `tximeta` and `SummarizedExperiment` -Read the `tximeta` package documentation [**here**](https://bioconductor.org/packages/release/bioc/manuals/tximeta/man/tximeta.pdf), and the package vignette by Love _et al._ [**here**](https://bioconductor.org/packages/devel/bioc/vignettes/tximeta/inst/doc/tximeta.html). -Read the `SummarizedExperiment` package documentation [**here**](http://bioconductor.org/packages/release/bioc/manuals/SummarizedExperiment/man/SummarizedExperiment.pdf), and the package vignette by Morgan _et al._ [**here**](https://www.bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html). + +Read the [`tximeta` package documentation (PDF)](https://bioconductor.org/packages/release/bioc/manuals/tximeta/man/tximeta.pdf), and the [package vignette by Love _et al._](https://bioconductor.org/packages/devel/bioc/vignettes/tximeta/inst/doc/tximeta.html). +Read the [`SummarizedExperiment` package documentation (PDF)](http://bioconductor.org/packages/release/bioc/manuals/SummarizedExperiment/man/SummarizedExperiment.pdf), and the [package vignette by Morgan _et al._](https://www.bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| | `tximeta`| [`tximeta()`](https://rdrr.io/bioc/tximeta/man/tximeta.html) | tximeta | Imports transcript-level estimates, attaches transcriptome annotation, and returns a `SummarizedExperiment` object | | `tximeta`| [`makeLinkedTxome()`](https://rdrr.io/bioc/tximeta/man/linkedTxome.html)| Make Linked Transcriptome | Sets up transcriptome annotation to be used by the `tximeta()` function (Only necessary if `tximeta()` fails to find annotation, like for non-human, non-mouse species data) | | `tximeta`| [`summarizeToGene()`](https://rdrr.io/bioc/tximeta/man/summarizeToGene.html)| Summarize to Gene | Takes a `SummarizedExperiment` that was set up by `tximeta` and summarizes transcript data to the gene-level | -| `SummarizedExperiment`| [`rowData()` `colData()`](https://www.rdocumentation.org/packages/SummarizedExperiment/versions/1.2.3/topics/SummarizedExperiment-class)| Col/Row Data| Accesses the row or column data from a `SummarizedExperiment` object| -| `SummarizedExperiment`| [`assay()` `assayNames()`](https://www.rdocumentation.org/packages/SummarizedExperiment/versions/1.2.3/topics/SummarizedExperiment-class)| Assay or AssayNames| Accesses the assay data or the names of the assays from `SummarizedExperiment` object| +| `SummarizedExperiment`| [`rowData()`; `colData()`](https://rdrr.io/bioc/SummarizedExperiment/man/SummarizedExperiment-class.html)| Row/Col Data| Accesses the row or column data from a `SummarizedExperiment` object| +| `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` @@ -83,24 +104,19 @@ Documentation for each of these packages can be accessed by clicking the package | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| [`stringr`](https://www.rdocumentation.org/packages/stringr/versions/1.3.1) |[`word()`](https://www.rdocumentation.org/packages/stringr/versions/1.3.1/topics/word) | Word | Extracts words from a character vector | -| [`readr`](https://www.rdocumentation.org/packages/readr/versions/1.3.0) |[`write_rds()`](https://www.rdocumentation.org/packages/readr/versions/1.3.0/topics/read_rds) | Write RDS | Writes data to a .RDS output file | -| [`dplyr`](https://www.rdocumentation.org/packages/dplyr/versions/0.7.8) | [`pull()`](https://www.rdocumentation.org/packages/dplyr/versions/0.7.8/topics/pull) | Pull | Extracts a variable (column) as a vector | -| [`pheatmap`](https://www.rdocumentation.org/packages/pheatmap/versions/1.0.10) | [`pheatmap()`](https://www.rdocumentation.org/packages/pheatmap/versions/1.0.10/topics/pheatmap) | Pretty heatmap | Plots clustered heatmaps | +| [`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 | ### Salmon -Read the Salmon tool documentation [**here**](https://salmon.readthedocs.io/en/latest/). +Read the [Salmon tool documentation](https://salmon.readthedocs.io/en/latest/). | Tool | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| Salmon | [`salmon index`](https://salmon.readthedocs.io/en/latest/salmon.html) | Salmon index | Builds a transcriptome index which is required for Salmon quantification (from the command line) | -| Salmon | [`salmon quant`](https://salmon.readthedocs.io/en/latest/salmon.html) | Salmon quantification | Runs Salmon’s quantification of transcript expression (from the command line) | +| Salmon | [`salmon index`](https://salmon.readthedocs.io/en/latest/salmon.html) | Salmon index | Builds a transcriptome index which is required for Salmon quantification (from the command line) | +| Salmon | [`salmon quant`](https://salmon.readthedocs.io/en/latest/salmon.html) | Salmon quantification | Runs Salmon’s quantification of transcript expression (from the command line) | -### Useful command line commands: - -![Useful Command Line Commands](diagrams/command-line-example.jpeg) - -Feel free to give these commands a try on your own! (Note that our example begins in the training-module directory.) diff --git a/module-cheatsheets/RNA-seq-cheatsheet.pdf b/module-cheatsheets/RNA-seq-cheatsheet.pdf index 2d60c8c8..a8ca86e1 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 e45ff3be..56fd5d9e 100644 --- a/module-cheatsheets/pathway-analysis-cheatsheet.md +++ b/module-cheatsheets/pathway-analysis-cheatsheet.md @@ -5,48 +5,67 @@ > Please note that these tables are not intended to tell you all the information you need to know about each command. > > The hyperlinks found in each piece of code will take you to the documentation for further information on the usage of each command. +Please be aware that the documentation will generally provide information about the given function's most current version (or a recent version, depending on how often the documentation site is updated). +This will usually (but not always!) match what you have installed on your machine. +If you have a different version of R or other R packages, the documentation may differ from what you have installed. + + + +**Table of Contents** + +- [`msigdbr`](#msigdbr) +- [AnnotationDbi](#annotationdbi) +- [Base `R`](#base-r) +- [`DESeq2`](#deseq2) +- [`enrichplot`](#enrichplot) +- [`clusterProfiler`](#clusterprofiler) +- [`GSVA`](#gsva) +- [`qusage`](#qusage) + + ### `msigdbr` -Read the `msigdbr` documentation [**here**](https://www.rdocumentation.org/packages/msigdbr/versions/7.1.1). +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://www.rdocumentation.org/packages/msigdbr/versions/7.1.1/topics/msigdbr)| geom vertical line| Retrieves the specified MSigDB dataset | +| `msigdbr`| [`msigdbr()`](https://rdrr.io/cran/msigdbr/man/msigdbr.html)| TODO | Retrieves the specified MSigDB dataset | + +### AnnotationDbi -### AnnotationDbi -Read the `AnnotationDbi` package vignette [**here**](http://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf). +Read the [`AnnotationDbi` package vignette (PDF)](http://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf). | Library/Package | Piece of Code | What it's called | What it does | |-----------------------------------------|---------------------------------------------|-------------------------|------------------------------------------------------------------------| -| `AnnotationDbi` | [`keytypes()`](https://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf) | Keytypes | Returns a character vector of column names/types of gene identifiers (e.g. `ENSEMBL` ) available in an `AnnotationDbi` package. | -| `AnnotationDbi` | [`mapIds()`](https://www.rdocumentation.org/packages/AnnotationDbi/versions/1.44.0/topics/AnnotationDb-objects) | Mapped IDs | Extracts the mapped IDs for a set of gene identifiers. The types of gene identifiers (e.g. `ENSEMBL` or `ENTREZ`) are supplied to arguments: `keytype` (type of gene identifiers we are providing in the `keys` argument) and `column` (type of gene identifiers we want returned). | +| `AnnotationDbi` | [`keytypes()`](https://rdrr.io/bioc/AnnotationDbi/man/AnnotationDb-class.html) | Keytypes | Returns a character vector of column names/types of gene identifiers (e.g. `ENSEMBL` ) available in an `AnnotationDbi` package. | +| `AnnotationDbi` | [`mapIds()`](https://rdrr.io/bioc/AnnotationDbi/man/AnnotationDb-class.html) | Mapped IDs | Extracts the mapped IDs for a set of gene identifiers. The types of gene identifiers (e.g. `ENSEMBL` or `ENTREZ`) are supplied to arguments: `keytype` (type of gene identifiers we are providing in the `keys` argument) and `column` (type of gene identifiers we want returned). | ### Base `R` -Read the Base `R` documentation [**here**](https://www.rdocumentation.org/packages/base/versions/3.5.1). +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://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/fisher.test)| 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`| [`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 | ### `DESeq2` -Read the `DESeq2` package documentation [**here**](https://bioc.ism.ac.jp/packages/3.8/bioc/manuals/DESeq2/man/DESeq2.pdf) and the package vignette by Love, Anders, and Huber [**here**](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html). +Read the [`DESeq2` package documentation (PDF)](https://www.bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf), and the [package vignette by Love, Anders, and Huber](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| `DESeq2` | [`results()`](https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/results) | Results | Returns the results table from a DESeq2 analysis | | `DESeq2` | [`lfcShrink()`](https://rdrr.io/bioc/DESeq2/man/lfcShrink.html) | Shrink Log Fold Changes | Adds shrunken log2 fold changes to the results of a `DESeqDataSet` object | -| `DESeq2` | [`resultsNames()`](https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/results) | Results Names | Returns the names of the estimated effects or coefficients of the `DESeq` model | +| `DESeq2` | [`results()`](https://rdrr.io/bioc/DESeq2/man/results.html) | Results | Returns the results table from a DESeq2 analysis | +| `DESeq2` | [`resultsNames()`](https://rdrr.io/bioc/DESeq2/man/results.html) | Results Names | Returns the names of the estimated effects or coefficients of the `DESeq` model | ### `enrichplot` -Read the `enrichplot` package documentation [**here**](https://bioconductor.org/packages/devel/bioc/manuals/enrichplot/man/enrichplot.pdf). +Read the [`enrichplot` package documentation (PDF)](https://bioconductor.org/packages/devel/bioc/manuals/enrichplot/man/enrichplot.pdf). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| @@ -56,28 +75,29 @@ Read the `enrichplot` package documentation [**here**](https://bioconductor.org/ ### `clusterProfiler` -Read the `clusterProfiler` package documentation [**here**](https://www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4). +Read the [`clusterProfiler` package documentation (PDF)](https://www.bioconductor.org/packages/release/bioc/manuals/clusterProfiler/man/clusterProfiler.pdf). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| `clusterProfiler` | [`enricher()`](https://www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4/topics/enricher) | Enricher | Performs a universal over-representation analysis for a given list of genes and gene sets or pathways | -| `clusterProfiler` | [`GSEA()`](https://www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4/topics/GSEA) | Gene Set Enrichment Analysis (GSEA) | Performs a universal gene set enrichment analysis on given preranked (sorted) named vector of statistics, where the names in the vector are gene identifiers of gene sets | +| `clusterProfiler` | [`enricher()`](https://rdrr.io/bioc/clusterProfiler/man/enricher.html) | Enricher | Performs a universal over-representation analysis for a given list of genes and gene sets or pathways | +| `clusterProfiler` | [`GSEA()`](https://rdrr.io/bioc/clusterProfiler/man/GSEA.html) | Gene Set Enrichment Analysis (GSEA) | Performs a universal gene set enrichment analysis on given preranked (sorted) named vector of statistics, where the names in the vector are gene identifiers of gene sets | ### `GSVA` -Read the `GSVA` package documentation [**here**](https://www.rdocumentation.org/packages/GSVA/versions/1.20.0). +Read the [`GSVA` package documentation](https://www.bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.html). | Library/Package | Piece of Code | What it's called | What it does | |-------------------------------|--------------------------------------------------------------|--------------------------------|--------------------------------------------------------------------------| -| `GSVA` | [`gsva()`](https://www.rdocumentation.org/packages/GSVA/versions/1.20.0/topics/gsva) | Gene Set Variation Analysis (GSVA) | Estimates gene set variation analysis enrichment scores on given gene expression matrix | +| `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()` | ### `qusage` -Read the `qusage` package documentation [**here**](https://www.rdocumentation.org/packages/qusage/versions/2.4.0). +Read the [`qusage` package documentation](https://rdrr.io/bioc/qusage/man/qusage.html). | Library/Package|Piece of Code| What it's called| What it does | |----------------|-------------|-----------------|---------------| -| `qusage` | [`read.gmt()`](https://www.rdocumentation.org/packages/qusage/versions/2.4.0/topics/read.gmt) | Read in `.gmt` files | Reads in gene set information from `.gmt` files | +| `qusage` | [`read.gmt()`](https://rdrr.io/bioc/qusage/man/read.gmt.html) | Read in `.gmt` files | Reads in gene set information from `.gmt` files | diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.pdf b/module-cheatsheets/pathway-analysis-cheatsheet.pdf index 5d2fc5ea..9c49650d 100644 Binary files a/module-cheatsheets/pathway-analysis-cheatsheet.pdf and b/module-cheatsheets/pathway-analysis-cheatsheet.pdf differ