Algorithms

add_att_b_sites Add attB Sites
add_fold_changes_to_variant Add Fold Changes
add_info_overlapping_genes Add Information from Overlapping Genes
alignment Create Alignment
amino_acid_changes Amino Acid Changes
annotate_conservation_score Annotate with Conservation Scores
annotate_exon_numbers Annotate with Exon Numbers
annotate_from_known_variants Annotate from Known Variants
annotate_nearby_gene Annotate with Nearby Gene Information
annotate_overlapping Annotate with Overlap Information
annotate_variant_flank Annotate with Flanking Sequences
assemble_sanger_sequences Assemble Sequences
associate_metadata Associate Data with Metadata
basic_variant_detection Basic Variant Detection
bisulfite_call_methylation_levels Call Methylation Levels
bisulfite_create_rrbs_track Create RRBS-fragment Track
bisulfite_read_mapping Map Bisulfite Reads to Reference
blast BLAST
blast_make_db Create BLAST Database
blast_ncbi BLAST at NCBI
boxplot Create Boxplot
bp_reaction Create Entry Clone (BP)
clustering_of_samples Hierarchical Clustering of Samples
cnv_detection CNV Detection
compare_sample_variant_tracks Compare Sample Variant Tracks
compare_variants_within_group Identify Shared Variants
consensus_sequence_extraction Extract Consensus Sequence
contig_read_mapping Map Reads to Contigs
convert_from_tracks Convert from Tracks
convert_to_dna Convert RNA to DNA
convert_to_rna Convert DNA To RNA
convert_to_tracks Convert to Tracks
coverage_analysis Whole Genome Coverage Analysis
create_combined_rnaseq_report Create Combined RNA-Seq Report
create_expression_browser Create Expression Browser
create_fc_from_expr_tracks_algo Create fold change track from expressions
create_heatmap_for_rnaseq Create Heat Map for RNA-Seq
create_histogram Create Histogram
create_sequence_statistics Sequence statistics
create_track_list Create Track List
create_venn_diagram_for_rnaseq Create Venn Diagram for RNA-Seq
denovo_assembly De Novo Assembly
detailed_mapping_report QC for Read Mapping
differential_expression_rna_seq Differential Expression for RNA-seq
differential_expression_two_groups Differential Expression in Two Groups
download_genome Download Genome
download_pfam_database Download Pfam Database
download_sequence_to_structure_db Download 3D Protein Structure Database
download_sra SRA Download
duplicate_mapped_reads_removal Duplicate Mapped Reads Removal
empirical_analysis_dge Empirical Analysis of DGE
experiment_to_track Create Track from Experiment
extract_annotations Extract Annotations
extract_overlapping_reads Extract Reads
extract_sequences Extract Sequences
filter_against_control_reads Remove Variants Present in Control Reads
filter_against_known_variants Filter against Known Variants
filter_annotation_names Filter Annotations on Name
filter_marginal_variants Remove Marginal Variants
filter_overlapping Filter Based on Overlap
filter_reference_variants Remove Reference Variants
find_open_reading_frames Find Open Reading Frames
find_primer_binding_sites Find Binding Sites and Create Fragments
fisher_exact_test Identify enriched variants in case vs control samples
fixed_ploidy_variant_detection Fixed Ploidy Variant Detection
gaussian_statistical_analysis Gaussian Statistical Analysis
gc_contents_graph_track Create GC Content Graph Track
gene_set_test Gene Set Test
go_analysis_expression_change Identify Differentially Expressed Gene Groups and Pathways
go_enrichment_variants GO Enrichment Analysis
graph_threshold Identify Graph Threshold Areas
identify_candidate_variants_new Filter Variants on Custom Criteria
import_metadata_rows Import Metadata rows into Metadata Table
import_tracks Import Tracks from File
kmer_tree_construction K-mer Based Tree Construction
link_to_structure Link Variants to 3D Protein Structure
local_realignment Local Realignment
low_frequency_variant_detection Low Frequency Variant Detection
lr_reaction Create Expression Clone (LR)
ma_plot Create MA Plot
mapping_graph_tracks Create Mapping Graph Tracks
merge_annotation_tracks Merge Annotation Tracks
merge_mappings Merge Read Mappings
merge_overlapping_pairs Merge Overlapping Pairs
ml_phylogeny Maximum Likelihood Phylogeny
model_testing Model Testing
motif_search Motif Search
mutation_tester_tool Identify Known Mutations from Mappings
new_sequence_list Sequence List
ngs_connector_import Import NGS sample reads
ngs_import_fasta Fasta High-Throughput Sequencing Import
ngs_import_genereader QIAGEN GeneReader Sequencing Import
ngs_import_illumina Illumina High-Throughput Sequencing Import
ngs_import_iontorrent Ion Torrent High-Throughput Sequencing Import
ngs_import_pacbio PacBio High-Throughput Sequencing Import
ngs_import_roche454 Roche 454 High-Throughput Sequencing Import (legacy)
ngs_import_sam Import SAM/BAM Mapping Files
ngs_import_sanger Sanger High-Throughput Sequencing Import
peak_shape_chip_seq_analysis Transcription Factor ChIP-Seq
pfam_domain_search Pfam domain search
predict_splice_site Predict Splice Site Effect
primer_pair_import Primer Pair Import
principal_component_for_rna_seq PCA for RNA-Seq
principal_components Principal Component Analysis
process_tagged_sequences Demultiplex Reads
proportion_statistical_analysis Proportion-based Statistical Analysis
read_mapping Map Reads to Reference
reference_assemble_sanger_sequences Assemble Sequences to Reference
remove_information_from_variants Remove Information from Variants
remove_orphan_reference_variants Remove Orphan Reference Variants
reverse_complement_sequence Reverse Complement Sequence
reverse_sequence Reverse Sequence
rna_seq RNA-Seq Analysis
sample_reads Sample Reads
secondary_peak_calling Secondary Peak Calling
sequencing_qc_report QC for Sequencing Reads
small_rna_annotate Annotate and Merge Counts
small_rna_sampling Extract and Count
spikein_control_import RNA Spike-ins
statistics_target_regions QC for Targeted Sequencing
structural_variant_detection InDels and Structural Variants
translate_to_protein Translate to Protein
tree_construction Create Tree
trim Trim Reads
trio_analysis TRIO analysis
xy_scatter_plot Create Scatter Plot

Subsections