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Total Results Found: 100

Total Results Found: 100

Past Seminars

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Confocal

2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...

R Introductory Series: Play with the theme to make this a bit nicer. Change font style to "Times". Change all font sizes to 12 pt font. Bold the legend title and the axes titles. Increase the size of the points on the plot to 2. Bonus: fill the points with color and have a black outline around each point.

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Bioinformatics

{{Sdet}} Solution{{Esum}} ggplot ( iris ) + geom_point ( aes ( Petal.Length , Petal.Width , fill = Species ), size = 2 , shape = 21 ) + coord_fixed ( ratio = 1 , ylim = c ( 0 , 2.75 ), xlim = c ( 0 , 7 )) + scale_y_continuous ( breaks = c ( 0 , 0.5 , 1 , 1.5 , 2 , 2.5 )) + scale_x_continuous ( breaks = c ( 0 , 1 , 2 , 3 , 4 , 5 , 6 , 7 )) + scale_fill_ Read More...

R Introductory Series 2023: Play with the theme to make this a bit nicer. Change font style to "Times". Change all font sizes to 12 pt font. Bold the legend title and the axes titles. Increase the size of the points on the plot to 2. Bonus: fill the points with color and have a black outline around each point.

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Bioinformatics

{{Sdet}} Solution{{Esum}} ggplot ( iris ) + geom_point ( aes ( Petal.Length , Petal.Width , fill = Species ), size = 2 , shape = 21 ) + coord_fixed ( ratio = 1 , ylim = c ( 0 , 2.75 ), xlim = c ( 0 , 7 )) + scale_y_continuous ( breaks = c ( 0 , 0.5 , 1 , 1.5 , 2 , 2.5 )) + scale_x_continuous ( breaks = c ( 0 , 1 , 2 , 3 , 4 , 5 , 6 , 7 )) + scale_fill_ Read More...

Data Visualization with R: stat = count

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Bioinformatics

Let's take a look at a bar plot constructed using the default stat="count" transformation. Below, we plot the number of tooth length measurements taken at each dose. Setting color="black& Read More...

Data Visualization with R: stat = count

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Bioinformatics

geom_bar() uses stat_count() by default: it counts the number of cases at each x position. --- ggplot2 documentation stat_count() requires mapping for either an x OR a y variable but not both. Read More...

Data Visualization with R: Using factors

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Bioinformatics

class(a1$dose) ## [1] "numeric" As it turns out, dose is really an experimental factor, so if we specify factor(dose) it will be interpreted as a categorical or discrete. Before fixing the x Read More...

Data Visualization with R: Using factors

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Bioinformatics

class ( a1 $ dose ) ## [1] "numeric" As it turns out, dose is really an experimental factor, so if we specify factor(dose) it will be interpreted as categorical or discrete. Before fixing the x axis Read More...

R Introductory Series: Coordinate systems

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Bioinformatics

ggplot2 uses a default coordinate system (the Cartesian coordinate system). This isn't super important until we want to do something like make a map (See coord_quickmap() ) or create a pie chart (See coord_ Read More...

Data Wrangling with R: Putting it all together

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Bioinformatics

Load in the comma separated file "./data/countB.csv" and save to an object named gcounts . {{Sdet}} Solution } gcounts `...1` colnames ( gcounts )[ 1 ] ## 1 Tspan6 703 567 867 71 970 242 ## 2 TNMD 490 482 18 342 935 469 ## 3 DPM1 921 797 622 661 8 500 ## 4 SCYL3 335 216 222 774 979 793 ## 5 FGR 574 574 515 584 941 344 ## 6 CFH 577 792 672 104 192 936 ## 7 FUCA2 798 766 995 27 756 546 ## 8 GCLC 822 874 923 705 667 522 ## 9 NFYA 622 793 918 868 334 64 {{Edet}} Plot the Read More...

Data Visualization with R: Histogram

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Bioinformatics

Understanding data distribution can help us decide appropriate downstream steps in analysis such as which statistical test to use. A histogram is a good way to visualize distribution. It divides the data into bins or Read More...

Data Visualization with R: Histogram

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Bioinformatics

Understanding data distribution can help us decide appropriate downstream steps in analysis such as which statistical test to use. A histogram is a good way to visualize distribution. It divides the data into bins or Read More...

Data Visualization with R: Modifying legends

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Bioinformatics

We can modify many aspects of the figure legend using the function guide() . Let's see how that works and go ahead and customize some theme arguments. Notice that the legend position is specified in Read More...

R Introductory Series 2023: Coordinate systems

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Bioinformatics

ggplot2 uses a default coordinate system (the Cartesian coordinate system). This isn't super important until we want to do something like make a map (See coord_quickmap() ) or create a pie chart (See coord_ Read More...

BTEP Lessons: Changing axes scales

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Bioinformatics

To change the y axis scale, we will need a specific function. These functions generally start with scale_y.... In our case we want to reverse our axis so that increasingly negative is going in Read More...

BTEP Lessons: Modifying legends

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Bioinformatics

We can modify many aspects of the figure legend using the function guide(). Let's see how that works and go ahead and customize some theme arguments. Notice that the legend position is specified in Read More...

BTEP Lessons: Expanding our ggplot2 template

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Bioinformatics

::: {.cell output-location='slide'} ggplot(exdata) + geom_point(aes(x=Number.of.Transcripts, y = Total.Counts, fill=Treatment), shape=21,size=3) + #can change labels of fill levels along with colors scale_fill_manual(values=c("purple& Read More...

BTEP Lessons: How can we modify colors?

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Bioinformatics

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

BTEP Lessons: How can we modify colors?

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Bioinformatics

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

NIH Intramural Sequencing Center (NISC)
Rockville, MD

Trans NIH Facility

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to Read More...

R Introductory Series: Colors

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Bioinformatics

ggplot2 will automatically assign colors to the categories in our data. Colors are assigned to the fill and color aesthetics in aes() . We can change the default colors by providing an additional layer to our Read More...

R Introductory Series: Nice plot example

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Bioinformatics

These steps can be used to create a publish worthy figure. For example, let's create a volcano plot of our differential expression results. A volcano plot is a type of scatterplot that shows statistical Read More...

Data Wrangling with R: Colors

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Bioinformatics

ggplot2 will automatically assign colors to the categories in our data. Colors are assigned to the fill and color aesthetics in aes() . We can change the default colors by providing an additional layer to our Read More...

Bioinformatics for Beginners 2022: Data Analysis Overview

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Bioinformatics

Data Analysis Overview RNASEQ - Data Analysis WorkFlow Mostly Computational intensive task requiring signigicant computer hardware. Quality Control Sample quality and consistency Is Trimming appropriate - quality/adaptors Alignment/Mapping Reference Target (Sequence and annotation) Read More...

Data Visualization with R: Question 4

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Bioinformatics

Play with the theme to make this a bit nicer. Change font style to "Times". Change all font sizes to 12 pt font. Bold the legend title and the axes titles. Increase the size Read More...

Data Visualization with R: Saving a non-ggplot

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Bioinformatics

Recall that we can use the ggsave command to save a ggplot. However, heatmaps generated using the pheatmap package are not ggplots, therefore we need to turn to either the image export feature (Figure 7) in Read More...

Data Visualization with R: Saving a non-ggplot

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Bioinformatics

Recall that we can use the ggsave command to save a ggplot. However, heatmaps generated using the pheatmap package are not ggplots, therefore we need to turn to either the image export feature (Figure 7) in Read More...

Data Visualization with R: stat = identity

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Bioinformatics

Above, we learned about the number of tooth length measurements taken at each dose and supplement combination using the default stat="count" transformation of geom_bar . But what if we want to specify Read More...

Data Visualization with R: stat = identity

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Bioinformatics

Above, we learned the number of tooth length measurements taken at each dose and supplement combination using the default stat_count transformation of geom_bar, but what if we want to specify and plot exactly Read More...

Data Visualization with R: Colors

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Bioinformatics

ggplot2 will automatically assign colors to the categories in our data. Colors are assigned to the fill and color aesthetics in aes() . We can change the default colors by providing an additional layer to our Read More...

Data Visualization with R: Lesson 4

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Bioinformatics

/* Whole document: */ body{ font-family: Times; font-size: 16pt; } Stat Transformations: Bar plots, box plots, and histograms Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar Read More...

Data Visualization with R: R Course FAQs

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Bioinformatics

Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types and the code Read More...

Data Visualization with R: R Course FAQs

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Bioinformatics

R Course FAQs Where can I find examples of different types of plots? The R Graph Gallery is a fantastic resource for R data visualization. The gallery can be used to explore different plot types Read More...

R Introductory Series 2023: Nice plot example

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Bioinformatics

These steps can be used to create a publish worthy figure. For example, let's create a volcano plot of our differential expression results. A volcano plot is a type of scatterplot that shows statistical Read More...

R Introductory Series 2023: Colors

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Bioinformatics

ggplot2 will automatically assign colors to the categories in our data. Colors are assigned to the fill and color aesthetics in aes() . We can change the default colors by providing an additional layer to our Read More...

Bioinformatics for Beginners 2022: Syllabus

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Bioinformatics

Syllabus for “Bioinformatics for Beginners" Instructors: Co-Instructors: To participate in these courses, you need a computer, reliable internet connection and a web browser. All classes and help sessions will be held online. This class Read More...

Data Visualization with R: Lesson5

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Bioinformatics

Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn how to work with the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify to Read More...

Data Visualization with R: Save as an R object

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Bioinformatics

Below, we assign the heatmap to the R object hm_ph. hm_ph {"x":{"data":[{"x":[4.875,2.875,null,2.875,2.875,null,2.875,1.75,null,1.75,1.75,null,1.75,1,null,1,1,null,1.75,2.5,null,2.5,2.5,null,2.5,2,null,2,2,null,2.5,3,null,3,3,null,2.875,4,null,4,4, Read More...

R Introductory Series 2023: ggplot2 Continued

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Bioinformatics

Objectives Review the grammar of graphics template. Learn about the statistical transformations inherent to geoms. Learn more about fine tuning figures with labels, legends, scales, and themes. Learn how to save plots with ggsave() . Review Read More...

R/Bioconductor Basics Workshop (2-day)

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Bioinformatics

10/22/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...

R/Bioconductor Basics Workshop (2-day)

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Bioinformatics

01/29/2015 - /* element spacing */ p, pre { margin: 0em 0em 1em; } /* center images and tables */ img, table { margin: 0em auto 1em; } p { text-align: justify; } tt, code, pre { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Read More...