Search Results for: Writing

The first example will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...

10/20/2023 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with statistical Read More...

10/18/2022 - In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with statistical Read More...

10/28/2020 - Register In partnership with the NIH Clinical Center's Biostatistics and Clinical Epidemiology Service (BCES), the NIH Library is offering a class to assist researchers in writing a manuscript. Participants will become familiar with Read More...

Top 10 errors in R and how to fix them. How to: Interpret Common Errors in R The Epidemiologist R Handbook: 47 Common Errors Modern Statistics with R: Debugging Common errors in R: An Empirical Investigation CODING Read More...

Top 10 errors in R and how to fix them. How to: Interpret Common Errors in R The Epidemiologist R Handbook: 47 Common Errors Modern Statistics with R: Debugging Common errors in R: An Empirical Investigation CODING Read More...

While we have learned how to use existing functions in R, we have not covered writing functions.

Versioning is a critical aspect of writing code for data analysis or software development. It enables tracking of changes and reverting if necessary. The ability to version is an essential skill whether working individually or Read More...

Optical Microscopy Core of the Experimental Immunology Branch (CCR/NCI) announces the introductory classes to Image J/FIJI: December 16th and 18th, 2020, 10 am to 4 pm with 1 hr break. Dr. Jan Wisniewski “Streamline Your Image Analysis: Read More...

11/12/2025 - In this hour and a half online training, attendees will be presented with simple ways to improve and optimize their code that can boost execution speed by orders of magnitude. Attendees will also learn Read More...

09/17/2025 - This hour and a half online training covers how to analyze and model data using interactive tools in MATLAB. Through live demonstrations and examples, attendees will learn to solve many steps in a data Read More...

11/12/2024 - In this hour and half online training, attendees will learn how to improve and optimize their MATLAB code to boost execution speed by orders of magnitude. The training covers common pitfalls in writing MATLAB Read More...

06/12/2024 - Macros are ways to use code to substitute in a value, and using macros makes a code in SAS easier to read and edit, less prone to errors, and allows it to run more Read More...

11/16/2023 - This class will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Read More...

09/14/2023 - In this 90-minute session, participants will learn to improve and optimize their MATLAB code to boost execution speed by orders of magnitude. The course covers common pitfalls in writing MATLAB code, explores the use Read More...

Picard is a set of command line tools for manipulating high- throughput sequencing (HTS) data and formats such as SAM/ BAM/CRAM and VCF. (mark pcr duplicates) Samtools provide various utilities for manipulating alignments in Read More...

Let's say you've got a very large FASTA or FASTQ file, and you want to run an analysis on it. Before working on the whole file, it can be useful to set up Read More...

#open R R #create project usethis::create_project(path = "MyNewProject", open = TRUE, rstudio = FALSE) #quit R q() v Creating 'MyNewProject/' v Setting active project to '/vf/users/emmonsal/R_on_Biowulf/MyNewProject' v Read More...

04/25/2023 - Macros are ways to use code to substitute in a value, and using macros makes a code in SAS easier to read and edit, less prone to errors, and allows it to run more Read More...

We recommend using RStudio Desktop, because it *provides a user-friendly environment with 4 pane views which makes it easier to use for examining data, writing scripts and running R analyses .* Additionally, RStudio Desktop provides a feature-rich Read More...

11/10/2020 - Link for ALL class sessions including help sessions. Register Meeting number: 172 866 2623 Password: NYy4m3V3i3* Dial in: 650-479-3207 The goal of this workshop is to teach novice programmers to write modular code Read More...

After this class, participants will Have obtained an appreciation for Jupyter Lab as a one-stop shop for organizing analysis steps, code, and output. Be aware of or able to describe the steps involved in using Read More...

After this class, participants will Have obtained an appreciation for Jupyter Lab as a one-stop shop for organizing analysis steps, code, and output. Be aware of or able to describe the steps involved in using Read More...

Its possible to run R code using the rpy2.ipython, which the user will have to install (see https://pypi.org/project/rpy2/). Assuming rpy2.ipython has been installed, load it in a Python Jupyter Read More...

Its possible to run R code using the rpy2.ipython, which the user will have to install (see https://pypi.org/project/rpy2/). Assuming rpy2.ipython has been installed, load it in a Python Jupyter Read More...

After this class, participants will be able to Have obtained an appreciation for Jupyter Lab as an one-stop shop for organizing analysis steps, code, and output. Be aware of or able to describe the steps Read More...

Table of Contents Start a Jupyter Lab session Jupyter Lab interface Changing between markdown and code Ways to access and use Jupyter Lab Install Jupyter Lab on Personal Computer Code and visualization Writing formatted text Read More...

The syntax for writing a function is as follows: function(x) { body # do something with x } where function is the function used to write the function, x is one or more arguments, and bodyis the Read More...

Let's say you've got a very large FASTA or FASTQ file, and you want to run an analysis on it. Before working on the whole file, it can be useful to set up Read More...

This class will introduce Git as a tool for versioning of code on local computer. At the of the class, participants will be able to Understand the importance of versioning code Describe version control Provide Read More...

This class will introduce Git as a version control system for files and code on local computer. After this session, participants will be able to Understand the importance of version control Describe version control Provide Read More...

nf-core is a community effort to generate a curated set of standardized, best-practice, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versatile workflow manager, Nextflow , and have been released under the Read More...

12/05/2024 - This one and a half hour online training will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be Read More...

12/03/2024 - This one and a half hour online training  will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek  Flow   Read More...

05/23/2024 - Versioning enables researchers to track changes in coding projects. This Coding Club introduces Git (https://git-scm.com), an open-source software used to perform versioning on a personal computer. At the end of this class, Read More...

03/05/2024 - This in-person workshop will show participants how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell Read More...

Who says Unix programmers don't have a sense of humor? Let me introduce cat , head , and tail . The cat command (short for "concatenate") is an extremely useful command for creating new files Read More...

06/29/2023 - Please join us for a special presentation about the Fred Hutchinson’s data journal to the cloud, including an innovative cloud platform (Cirro:  https://cirro.bio/ ) to streamline data collection, Read More...

05/10/2022 - Overview Python is one of the preferred programming languages for scientists to solve a wide variety of biological problems. We find that many scientists who come to Software Carpentry workshops use Python and want Read More...

Installing RStudio Desktop on the Mac We recommend using RStudio Desktop, because it *provides a user-friendly environment with 4 pane views which makes it easier to use for examining data, writing scripts and running R analyses .* Read More...

Now that you know the basics, you may be interested in creating a function that will plot different sets of data the same way using ggplot2. However, tidyverse functions use something called "tidy evaluation Read More...

Now that authentication is setup, we can return to the remote. This command will push the changes from our local repository to the repository on GitHub: git push origin main If you set up a Read More...

Who says Unix programmers don't have a sense of humor? Let me introduce cat, head, and tail. The cat command (short for "concatenate") is an extremely useful command for creating new files Read More...

Open the blank git_in_rstudio.R script and check the box under the "Staged" column next to the script git_in_rstudio.R and git_in_rstudio.Rproj to stage these two Read More...

In this session, participants will practice generating a gene expression matrix for the HBR-UHR data. Sign onto Biowulf and change into the /data/user/hbr_uhr_b4b folder. Solution ssh user@biowulf.nih.gov Read More...

Clustering is used to group cells by similar transcriptomic profiles. Seurat uses a graph based clustering method. You can read more about it here . The first step is to compute the nearest neighbors of each Read More...

Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples. Throughout this tutorial we Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

Lesson 4: Useful Unix For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 3 Review Biowulf is the high performance computing cluster at NIH. When you apply for a Biowulf account Read More...

Alignment RNASeq Mapping Challenges The majority of mRNA derived from eukaryotes is the result of splicing together discontinuous exons, and this creates specific challenges for the alignment of RNASEQ data. Mapping Challenges Reads not perfect Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinfo environment. conda activate bioinfo Then create a new directory for files we will be working with today in Read More...

Lesson 3: R Project Management and renv Learning objectives Discuss the importance of reproducibility Learn ways to make R analyses more reproducible Learn how to set up and organize an R project Learn how to use Read More...

Managing Bioinformatics Projects with Jupyter Lab Learning Objectives After this class, participants will have obtained the foundation needed to start using Jupyter Lab as an all-in-one place to maintain code, output, and other description of Read More...

12/20/2016 - ABOUT THE COURSE R is a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series Read More...

11/22/2016 - ABOUT THE COURSE R is a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series Read More...

11/09/2015 - A Short Course in R for Biologists "A Short Course in R for Biologists" is a two-day course given in four three-hour sessions entitled: Introduction to R, Introduction to Bioconductor, Introduction to Read More...

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...

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...

Changes to a coding project (including scripts, data, and other content) should be saved periodically, similar to clicking on the "save" button to periodically save changes when constructing a word document. This is Read More...