Introduction | Getting started | Installation | Loading package and documentation | Overview of workflow templates | Use workflow templates | Load a workflow | Run and visualize workflow | Additional workflow templates on GitHub | Useful functionalities | Create workflow templates interactively | Return paths to sample data | Analysis steps in selected workflows | Generic template | RNA-Seq workflow | ChIP-Seq Workflow | VAR-Seq Workflow | Ribo-Seq Workflow | scRNA-Seq Workflow | BLAST Workflow | Cheminformatics Workflow | Version information | Funding | References

Introduction | Design overview | CL interface (CLI) | Workflow templates | Other functionalities | Quick start | Installation | Five minute tutorial | Directory structure | The targets file | Single-end (SE) data | Paired-end (PE) data | Sample comparisons | Detailed tutorial | Initialization | Constructing workflows | Stepwise construction | Step 1: R step | Step 2: CL step | Step 3: CL with input from previous step | Step 4: R with input from previous step | Load workflow from R or Rmd scripts | Define workflow steps in R Markdowns | Running workflows | Overview | Module system | Parallel evaluation | Visualize workflows | Report generation | Scientific reports | Technical report | Converting workflows to Bash and Rmd | R Markdown script | Bash script | Restarting and resetting workflows | Additional utilities | Accessor methods | General information | Slot data | CL and R code | R environment | Subsetting workflows | Replacement methods | Changing parameters | Changes to R steps | Replacing workflow steps | CWL specifications | CWL CommandLineTool | CWL Workflow | CWL input values | Mappings among cwl, yml and targets | Assembly of CL calls from three files | Auto-creation of CWL files | Expected CL syntax | createParam Function | Example with targets file | Utilities for CWL files | Printing components | Subsetting the CL strings | Replacing existing arguments | Adding new arguments | Editing output parameters | Workflow step classes | SYSargs2 class | LineWise Class | Supplemental Material | Examples of CL software | Data analysis functionalities | Project initialization | Read Preprocessing | Preprocessing with preprocessReads function | Preprocessing with TrimGalore! | Preprocessing with Trimmomatic | FASTQ quality report | NGS Alignment software | HISAT2 | Tophat2 | Bowtie2 | BWA-MEM | Rsubread | gsnap | BAM file viewing in IGV | Read counting for mRNA profiling experiments | Read and alignment stats | Read counting for miRNA profiling experiments | Correlation analysis of samples | DEG analysis with edgeR | DEG analysis with DESeq2 | Venn Diagrams | GO term enrichment analysis of DEGs | Obtain gene-to-GO mappings | Batch GO term enrichment analysis | Plot batch GO term results | Clustering and heat maps | Version information | Funding | References

Introduction | Overview | Experimental design | Workflow steps | Load workflow environment | Input data: targets file | Quick start | Load packages | Read preprocessing | With preprocessReads | With Trimmomatic | FASTQ quality report | Short read alignments | Read mapping with HISAT2 | HISAT2 mapping | Alignment stats | Viewing BAM files in IGV | Read quantification | Gene annotation database | Read counting with summarizeOverlaps | Sample-wise clustering | Analysis of DEGs | Run edgeR | Add gene descriptions | Plot DEG results | Venn diagrams of DEG sets | GO term enrichment analysis | Obtain gene-to-GO mappings | Batch GO term enrichment analysis | Plot batch GO term results | Clustering and heat maps | Workflow session information | Additional details | Running workflows | Parallelization on clusters | CL tools used | Session info | Funding | References

Introduction | Overview | Experimental design | Workflow steps | Load workflow environment | Input data: targets file | Quick start | Required packages and resources | FASTQ quality reports | With FastQC | With seeFastq | Read preprocessing | Read trimming with Trimmomatic | Preprocessing with preprocessReads | Read mapping with BWA-MEM | Index and dictionary files | Mapping reads with BWA-MEM | Read and alignment stats | Sym links for viewing BAM files in IGV | Variant calling with GATK | Step1: fastq to ubam | Step2: Merge bam and ubam | Step3: Sort bam files by genomic coordinates | Step4: Mark duplicates | Step5: Fixing tags | Step6: HaplotypeCaller | Step7: Import all gvcfs | Step8: Joint genotyping (cohort calling) | Step9: Hard filter (cohort) variants | Step10: Extract variants per sample | Inspect VCF files | Import VCFs into R | Filter variants in R | Filter statistics | Annotate variants | Annotate variants with SnpEff | Combine annotation results among samples | Summary table of variants | Plot raw variants table by consequence | Plot variants stats | Compare high-impact variants by group | Venn diagram of variants | Plot variants programmatically | Non-Synonymous Variants | Pathway Enrichment | Drug-Target Analysis | Version information | Additional details | Running workflows | Parallelization on clusters | Visualize workflow | Checking workflow status | Accessing logs report | Tools used | Report Session Info | Funding | References

Introduction | Getting Started | Installation | Loading the Package and Documentation | Quick Tutorial | Examples | Loading User Supplied PubChem BioAssay Data | Prebuilt Database Example: Investigate Activity of a Known Drug | Identify Target Selective Compounds | Cluster Compounds by Activity Profile | Analyze and Load Raw Screening Data | Custom SQL Queries | Building PubChem BioAssay Database | Version Information | Funding | References

Introduction | Overview | Experimental design | Workflow steps | Load workflow environment | Input data: targets file | Quick start | Load packages | Load data | Simple count visulization | Create Seurat object | QC of cells | Filter cells | Normalization | Find highly variable genes | Scaling | PCA | Plot PCA results | Find optimal PCs | Clustering | Visualize clusters with UMAP/tSNE | Find cluster biomarkers | Visualize markers | Classify cell types | Workflow session | Manage the workflow | About the workflow | Tools used | Session Info

Workflow environment | Create workflow environment | Construct workflow | Step 1: Load packages | Step 2: Export tabular data to files | Step 3: Compress data | Step 4: Uncompress data | Step 5: Import tabular files and visualize data | Version Information | Automated routine | CL tools used | Session Info | References

About this template | Workflow environment | Step 1: Load packages | Step 2: Test BLAST install | Step 3: BLASTable database | Step 4: BLAST search | Step 5: View top hits | Version Information | Automated routine | CL tools used | Session Info

About the template | Workflow environment | Step 1: Load packages | Step 2: Import molecule structures | Step 3: Visualize molecule structures | Step 4: Physicochemical properties | Step 5: Box plots of properties | Step 6: Structural descriptors | Step 7: Removal of identical fingerprint sets | Step 8: Similarity compute | Step 9: Hierarchical clustering | Step 10: PCA | Step 11: Include heatmap | Version information | Automated routine | CL tools used | Session Info

Introduction | Overview | Experimental design | Workflow steps | Load workflow environment | Input data: targets file | Quick start | Load packages | Read preprocessing | FASTQ quality report | Preprocessing with preprocessReads function | Alignments | Read mapping with Bowtie2 | Read and alignment stats | Create symbolic links for viewing BAM files in IGV | Utilities for coverage data | Rle object stores coverage information | Resizing aligned reads | Naive peak calling | Plot coverage for defined region | Peak calling with MACS2 | Merge BAM files of replicates prior to peak calling | Peak calling without input/reference sample | Peak calling with input/reference sample | Identify consensus peaks | Annotate peaks with genomic context | Annotation with ChIPseeker package | Annotation with ChIPpeakAnno package | Count reads overlapping peaks | Differential binding analysis | GO term enrichment analysis | Motif analysis | Parse DNA sequences of peak regions from genome | Motif discovery with BCRANK | Version Information | Running workflow | Interactive job submissions in a single machine | Parallelization on clusters | Visualize workflow | Checking workflow status | Accessing logs report | Tools used | Session Info | Funding | References

Introduction | Experimental design | Workflow environment | Load packages and sample data | Generate workflow environment | Experiment definition provided by targets file | Required packages and resources | Read preprocessing | Preprocessing with preprocessReads function | FASTQ quality report | Alignments | Read mapping with HISAT2 | HISAT2 mapping | Read and alignment stats | Create symbolic links for viewing BAM files in IGV | Read distribution across genomic features | Obtain feature types | Count and plot reads of any length | Count and plot reads of specific lengths | Adding custom features to workflow | Predicting uORFs in 5' UTR regions | Adding custom features to other feature types | Predicting sORFs in intergenic regions | Genomic read coverage along transripts or CDSs | Binned CDS coverage to compare many transcripts | Coverage upstream and downstream of start and stop codons | Combined coverage for both binned CDS and start/stop codons | Nucleotide level coverage along entire transcripts/CDSs | Read quantification per annotation range | Read counting with summarizeOverlaps in parallel mode using multiple cores | Sample-wise correlation analysis | Analysis of differentially expressed genes with edgeR | Plot DEG results | Venn diagrams of DEG sets | GO term enrichment analysis of DEGs | Obtain gene-to-GO mappings | Batch GO term enrichment analysis | Plot batch GO term results | Differential ribosome loading analysis (translational efficiency) | Clustering and heat maps | Version Information | Running workflow | Interactive job submissions in a single machine | Parallelization on clusters | Visualize workflow | Checking workflow status | Accessing logs report | Tools used | Report Information | Funding | References

Introduction | Installation | Limitations on Windows | User Manual in ChemmineR Vignette | SWIG Interface (For R developers) | Version Information | Funding | References

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Introduction | Getting Started | Installation | Loading the Package and Documentation | Five Minute Tutorial | OpenBabel Functions | Overview of Classes and Functions | Molecular Structure Data | Structure Descriptor Data | Import of Compounds | SDF Import | SMILES Import | Export of Compounds | SDF Export | SMILES Export | Format Interconversions | Splitting SD Files | Streaming Through Large SD Files | Storing Compounds in an SQL Database | Loading Data | Updates | Duplicate Descriptors | Searching | Using Search Results | Pre-Built Databases | Working with SDF/SDFset Classes | Molecular Property Functions (Physicochemical Descriptors) | Bond Matrices | Charges and Missing Hydrogens | Ring Perception and Aromaticity Assignment | Rendering Chemical Structure Images | R Graphics Device | Data Tables | Online with ChemMine Tools | Similarity Comparisons and Searching | Maximum Common Substructure (MCS) Searching | AP/APset Classes for Storing Atom Pair Descriptors | Large SDF and Atom Pair Databases | Pairwise Compound Comparisons with Atom Pairs | Similarity Searching with Atom Pairs | FP/FPset Classes for Storing Fingerprints | Atom Pair Fingerprints | Fingerprint E-values | Pairwise Compound Comparisons with PubChem Fingerprints | Similarity Searching with PubChem Fingerprints | Visualize Similarity Search Results | Clustering | Clustering Identical or Very Similar Compounds | Binning Clustering | Jarvis-Patrick Clustering | Multi-Dimensional Scaling (MDS) | Clustering with Other Algorithms | Searching PubChem | Get Compound SDF from PubChem by Id | Get Compound SDF from PubChem by InChIkey | Get Compound CID from PubChem by InChI | Search a SMILES Query in PubChem | Search an SDF Query in PubChem | ChemMine Tools R Interface | Launch a Job | View Job Result in Browser | Version Information | Funding | References

Introduction | Installation | Quick Overview | Documentation | MCS of Two Compounds | Data Import | Compute MCS | Class Usage | FMCS of Two Compounds | FMCS Search Functionality | Clustering with FMCS | Version Information | References

Introduction | Initialization | Creating a Searchable Database | Queries | Adding New Compounds | Performance Tests | Clustering | Customization | Version Information | Funding | References