From 57c20ad7105ffafe5a089a27a02c8dd7e13270c8 Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 15:48:45 -0400 Subject: [PATCH 1/9] Fill in TODO for msigdbr() --- module-cheatsheets/pathway-analysis-cheatsheet.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.md b/module-cheatsheets/pathway-analysis-cheatsheet.md index 56fd5d9e..a1f3e60b 100644 --- a/module-cheatsheets/pathway-analysis-cheatsheet.md +++ b/module-cheatsheets/pathway-analysis-cheatsheet.md @@ -32,7 +32,7 @@ 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 From 9da70225a16b98d0e8de8ca59ba620c4172d3566 Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 15:48:57 -0400 Subject: [PATCH 2/9] Add setdiff() to Base R table --- module-cheatsheets/pathway-analysis-cheatsheet.md | 1 + 1 file changed, 1 insertion(+) diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.md b/module-cheatsheets/pathway-analysis-cheatsheet.md index a1f3e60b..9d853e85 100644 --- a/module-cheatsheets/pathway-analysis-cheatsheet.md +++ b/module-cheatsheets/pathway-analysis-cheatsheet.md @@ -50,6 +50,7 @@ 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) |
From e8f86c927bc08b2077ac1bb4ff71d3b361be6bf2 Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 15:50:04 -0400 Subject: [PATCH 3/9] Comment out DESeq2 section --- module-cheatsheets/pathway-analysis-cheatsheet.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.md b/module-cheatsheets/pathway-analysis-cheatsheet.md index 9d853e85..ac31adea 100644 --- a/module-cheatsheets/pathway-analysis-cheatsheet.md +++ b/module-cheatsheets/pathway-analysis-cheatsheet.md @@ -54,6 +54,7 @@ Read the [Base `R` documentation](https://rdrr.io/r/). + + ### `enrichplot` Read the [`enrichplot` package documentation (PDF)](https://bioconductor.org/packages/devel/bioc/manuals/enrichplot/man/enrichplot.pdf). From 750e99aea8765508ff6e7ee1c14433b27ed46e0b Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 15:50:54 -0400 Subject: [PATCH 4/9] Clarification re: gsvaParam() --- module-cheatsheets/pathway-analysis-cheatsheet.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.md b/module-cheatsheets/pathway-analysis-cheatsheet.md index ac31adea..e63f0be2 100644 --- a/module-cheatsheets/pathway-analysis-cheatsheet.md +++ b/module-cheatsheets/pathway-analysis-cheatsheet.md @@ -95,7 +95,7 @@ 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` From 787545c8eda964ae50deed88da56f96435d36331 Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 16:07:01 -0400 Subject: [PATCH 5/9] Add the matrix operations used in the heatmap notebook --- module-cheatsheets/RNA-seq-cheatsheet.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/module-cheatsheets/RNA-seq-cheatsheet.md b/module-cheatsheets/RNA-seq-cheatsheet.md index 9861deab..a1dd7a02 100644 --- a/module-cheatsheets/RNA-seq-cheatsheet.md +++ b/module-cheatsheets/RNA-seq-cheatsheet.md @@ -37,6 +37,7 @@ 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 | @@ -108,6 +109,15 @@ Documentation for each of these packages can be accessed by clicking the package | [`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 | +### `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 devations | Estimates the standard deviations for each row in a matrix | + ### Salmon From 69062e43e6e173c34f4e83e8a7b74d28048ae73a Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 16:13:22 -0400 Subject: [PATCH 6/9] Swap ComplexHeatmap for pheatmap --- module-cheatsheets/RNA-seq-cheatsheet.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/module-cheatsheets/RNA-seq-cheatsheet.md b/module-cheatsheets/RNA-seq-cheatsheet.md index a1dd7a02..90e7649f 100644 --- a/module-cheatsheets/RNA-seq-cheatsheet.md +++ b/module-cheatsheets/RNA-seq-cheatsheet.md @@ -99,7 +99,7 @@ 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. @@ -108,7 +108,16 @@ 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). From 65f53c1c9825b7596bf73e5d8795892174619c87 Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 16:20:43 -0400 Subject: [PATCH 7/9] Run doctoc on updated cheatsheets --- module-cheatsheets/RNA-seq-cheatsheet.md | 4 +++- module-cheatsheets/pathway-analysis-cheatsheet.md | 1 - 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/module-cheatsheets/RNA-seq-cheatsheet.md b/module-cheatsheets/RNA-seq-cheatsheet.md index 90e7649f..8638263d 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) diff --git a/module-cheatsheets/pathway-analysis-cheatsheet.md b/module-cheatsheets/pathway-analysis-cheatsheet.md index e63f0be2..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) From f4d1e3d2774c6c532aa3bc687fd541cfedfdec3d Mon Sep 17 00:00:00 2001 From: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com> Date: Wed, 7 Aug 2024 17:07:03 -0400 Subject: [PATCH 8/9] Update PDF copies of RNA-seq and pathway analysis cheatsheets --- module-cheatsheets/RNA-seq-cheatsheet.pdf | Bin 124132 -> 131865 bytes .../pathway-analysis-cheatsheet.pdf | Bin 90892 -> 84774 bytes 2 files changed, 0 insertions(+), 0 deletions(-) diff --git a/module-cheatsheets/RNA-seq-cheatsheet.pdf b/module-cheatsheets/RNA-seq-cheatsheet.pdf index a8ca86e13136709f6466e141b98315bc47ea8d64..1893d95b6fdc01d685c30f368b7217264ba41e3a 100644 GIT binary patch delta 67451 zcmZ6yV|XAz^Di26V`pP)W81cE+u9_vu{XAD+s4MWv%$tTZr=ZU&bjxV57Slk>+Y(a zXKK2-yJr6Wfldp7iCux_U}j=uW8sL~#{1uF0~ja=I3yDXJ3U7NKLllhJ%k=TD+>`T zI~zSG2NxHI9vp+HnTsnCgNcKkqpg{zrJ0edoslCyKb)Dpse`dK98-c)y)X+0Cp{Yx zD=RBK6Z2OmA|@6_dgd>Hjpe_<|IuP+