Package: systemPipeRdata 2.17.2

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 | 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 | 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