Explore UAB

Learn Python
 Introduction to Python with interactive examples 
Python for Data Science  Learn applications of Python for data science 
Python for Data Science Certificate   Earn a free code academy certificate in Python for data science 
Learn R  Tutorials on R with interactive examples from Code Academy 
Bash and Shell Tutorial  Bash command line basics with interactive examples 
Command Line Basic  Tutorial on command line basics from Code Academy 
Foundations of Coding  The basics of programming and coding from the Odin Project 
Gladstone Bioinformatics Workshops Workshops covering methods such as RNA-seq, pathway analysis, and whole genome sequencing 
Machine Learning Workshop Google's open resource machine learning lessons and resources 

HDOCK Protein-protein and protein-DNA/RNA docking  
OpenCell Proteome-scale measurements of human protein localization and interactions 
BioGRID Biomedical interaction repository 
STRING Protein Interaction Networks & functional Enrichment Analysis 
PRIDE Proteomics identification database 
The Human Protein Atlas Open access repository of human genes & proteins 
AlphaFold Protein structure database 
UniProt Protein sequence and function repository  
The Lasseigne Lab Dr. Lasseigne's lab website contains resources for data analysis for brain sciences. 
Dropviz.org Single-cell transcriptomic data from mouse animal models 
Enrichr Promoter analyses and gene ontology for differentially expressed genes 
Jaspar Transcription factor binding sites 
Cell Profiler Cell image analysis software 
KEGG Pathway Database Pathways for molecular interactions in metabolism, genetics, and more 
WikiPathways Open platform database for biological pathways 
Reactome Visualization, interpretation, and analysis of genomic and system biology data  
GTEx Tissue-specific gene expression and regulation database   
UCSC Genome Browser  Interactively visualize genomic data 
miRMaster comprehensive analysis framework for sncRNA-seq data
CAP-MIRSEQ A comprehensive analysis pipeline for deep microRNA sequencing
Cell Ranger Analysis pipelines for single-cell data
SEURAT R toolkit for single-cell genomics 
SCANPY Python single-cell analysis pipelines
Monocle 3 Analysis toolkit for single-cell RNA-seq
Velocyto Estimating RNA expression dynamics in single-cell RNA sequencing data
Signac R package for analysis of single-cell chromatin data
Burrows-Wheeler Aligner RNA-seq alignment software
Bowtie 2 RNA-seq alignment software
minimap 2 Pairwise aligner for genomic and spliced nucleotide sequences
TopHat A spliced read mapper for RNA-seq
Salmon  Tool for quantifying expression of RNA transcripts in RNA-seq data
Babraham Bioinformatics Map bisulfite-treated sequencing reads to a genome of interest and performs methylation calls
methylKit R package for DNA methylation analysis
BSMAP for Methylation Short read mapping program for bisulfite sequencing in DNA methylation
Bioconductor Analyze, manage, and store bisulfite sequencing data
STAR RNA-seq aligner

Statistics, Rigor, & Reproducibility
NIH Grants & Funding NIH resources for publishing research, writing grant applications, and policies
NINDS Preparing Your Research Plan NIH resources for rigorous study design and transparent reporting
SAMPL Guidelines Basic Statistica Reporting for Biomedical Writing: Statistical Analyses and Methods in the Published Literature (SAMPL)
ARRIVE Guidelines Author checklist of minimum items to include in a manuscript
STAR Methods CellPress Methods Guide for Authors
PLOS Submission Guideline Resources from PLOS One: Writing Center, Submission System, Getting started Guide, and Guideline for revisions
How to Report Statistics PLOS resource on how to ensure appropriateness and rigor, avoid flexibility, and ethical result presentation
Center for Open Science TOP guidelines created by journals, funding sources, and societies with ideal practices for transparent research
Zenodo Distribution of big data management tools with digital library capabilities from CERN

F-Series Grant Writing
Official NIH NRSA Guidelines (F31) Official guidelines for preparing an F31 submission
NIH Application Guide NIH Central Resource for Grants and Funding Information
Grants.gov Search for previously or currently funded NIH projects 
Tips on Writing NRSA Proposals Advice from NRSA Reviewers on how to write a fundable proposal from
How to write a strong NRSA grant A primer on F31 process and crowdsourced tips from UCLA
UAB F-series Samples Samples of F-series grants submitted and funded from UAB students & faculty 
F-series Check List A guide for crafting and writing an NIH NRSA F-series training grants (F30, F31, F32)
Find your Officer or Specialist UAB Search tool for identifying the appropriate program officer or specialist for your funding agency and specialty 
Formatting Guidelines for NIH Proposals Format for NIH proposal attachments (e.g. citations, fonts, images, etc)
If you have information on additional resources email marycooper@uab.edu