align_dna | Alignment of DNA-seq reads |
annotate_peaks | Annotation of peaks |
build_index | Build insex for HISAT2 |
cc_chip | Create cross-correlation plots for ChIP-seq data |
chain | LiftOver chain file in rda format for conversion from hg38 to... |
check_sample | Check that targets file contains the necessary info in the... |
consensus_peaks | Consensus peaks |
create_bw | Create bigwig files |
deseq2_analysis | Run DESeq2 analysis on ChIP/ATAC-seq count data |
exploratory_analysis | Exploratory analysis of DESeq2 data |
fl_atac | Create fragment size plots for ATAC-seq data |
make_MA | Create MA plot |
make_PCA | Create PCA plot for transformed data |
make_scree | Create scree plot from prcomp data |
peak2Granges | File conversions |
pipe | Pipe operator |
plot_peaksummary | Plots of peak width and distance to TSS |
qc_alignment | Generate some alignment statistics on reads |
qc_alignment2 | Perform alignment statistics on reads |
run_atac | Run ATAC-seq analysis |
run_chip | Run ChIP-seq analysis |
run_fastqc | QC reports for fastq files using FastQC |
run_featurecounts | Count reads in bam files using featureCounts |
run_great | GREAT analysis |
run_hisat2 | Wrapper script to run HISAT2. |
run_macs2 | Perform peakcalling with MACS2 |
run_multiqc | Generate MultiQC report for FastQC |
run_sambambadup | Mark duplicates in BAM file |
run_samsort | Wrapper scripts for SAMtools functions |
sanity_check | Import the metadata and check it is correct |
shift_bam | Shift ATAC-seq reads |
trim_fastq | An R-based wrapper for fastp |
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