The Rainfall plot
Rainfall plot tools
GSuite HyperBrowser tools
Create a GSuite of genomic tracks
Customize a GSuite
Quantitative overview of GSuites
Statistical analysis of GSuites
Visual analysis of GSuites
Domain-specific analysis
GSuite documentation
Planned tools (Still in developmen or on hold)
Not part of current submission
HyperBrowser analysis
Statistical analysis of tracks
Visual analysis of tracks
Genomic variation analysis
Specialized analysis of tracks
Text-based analysis interface
HyperBrowser track processing
HyperBrowser track repository
Customize tracks
Generate tracks
Format and convert tracks
Export and import tracks
GTrack tools
Article/domain-specific tools
Skeletal RNA interaction map
The differential disease regulome
MCFDR
Monte Carlo null models
Transcription factor analysis
Gene tools
Variant melting profiles
HyperBrowser internal tools
Admin of genomes and tracks
Development tools
Assorted tools
User bookmarks
Exam analysis
Standard Galaxy tools
Get Data
Upload File from your computer
UCSC Main table browser
UCSC Test table browser
UCSC Archaea table browser
BX main browser
EBI SRA ENA SRA
BioMart Central server
BioMart Test server
CBI Rice Mart rice mart
GrameneMart Central server
modENCODE fly server
Flymine server
Flymine test server
Ratmine server
YeastMine server
metabolicMine server
Wormbase server
Wormbase test server
EuPathDB server
EncodeDB at NHGRI
EpiGRAPH server
EpiGRAPH test server
HbVar Human Hemoglobin Variants and Thalassemias
GenomeSpace import from file browser
Send Data
Perform genome analysis and prediction with EpiGRAPH
Perform genome analysis and prediction with EpiGRAPH Test
ENCODE Tools
Gencode Partition an interval file
Random Intervals create a random set of intervals
Lift-Over
Convert genome coordinates between assemblies and genomes
Text Manipulation
Add column to an existing dataset
Compute an expression on every row
Concatenate datasets tail-to-head
Cut columns from a table
Merge Columns together
Convert delimiters to TAB
Create single interval as a new dataset
Change Case of selected columns
Paste two files side by side
Remove beginning of a file
Select random lines from a file
Select first lines from a dataset
Select last lines from a dataset
Trim leading or trailing characters
Filter on ambiguities in polymorphism datasets
Filter and Sort
Filter data on any column using simple expressions
Sort data in ascending or descending order
Select lines that match an expression
GFF
Extract features from GFF data
Filter GFF data by attribute using simple expressions
Filter GFF data by feature count using simple expressions
Join, Subtract and Group
Join two Datasets side by side on a specified field
Compare two Datasets to find common or distinct rows
Subtract Whole Dataset from another dataset
Group data by a column and perform aggregate operation on other columns.
Convert Formats
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment
AXT to FASTA Converts an AXT formatted file to FASTA format
AXT to LAV Converts an AXT formatted file to LAV format
BED-to-GFF converter
FASTA-to-Tabular converter
GFF-to-BED converter
LAV to BED Converts a LAV formatted file to BED format
Maf to BED Converts a MAF formatted file to the BED format
MAF to Interval Converts a MAF formatted file to the Interval format
MAF to FASTA Converts a MAF formatted file to FASTA format
Tabular-to-FASTA converts tabular file to FASTA format
FASTQ to FASTA converter
Wiggle-to-Interval converter
GTF-to-BEDGraph converter
Wig-to-bigWig converter
BED-to-bigBed converter
Extract Features
Fetch Sequences
Extract Genomic DNA using coordinates from assembled/unassembled genomes
Fetch Alignments
Extract Pairwise MAF blocks given a set of genomic intervals
Extract MAF blocks given a set of genomic intervals
Split MAF blocks by Species
Stitch MAF blocks given a set of genomic intervals
Stitch Gene blocks given a set of coding exon intervals
MAF Coverage Stats Alignment coverage information
Join MAF blocks by Species
Filter MAF blocks by Species
Extract MAF by block number given a set of block numbers and a MAF file
Reverse Complement a MAF file
Filter MAF by specified attributes
Get Genomic Scores
Wiggle-to-Interval converter
Aggregate datapoints such as phastCons, GERP, binCons, and others for a set of genomic intervals
Compute phastOdds score for each interval
Operate on Genomic Intervals
Intersect the intervals of two datasets
Subtract the intervals of two datasets
Merge the overlapping intervals of a dataset
Concatenate two datasets into one dataset
Base Coverage of all intervals
Coverage of a set of intervals on second set of intervals
Complement intervals of a dataset
Cluster the intervals of a dataset
Join the intervals of two datasets side-by-side
Get flanks returns flanking region/s for every gene
Profile Annotations for a set of genomic intervals
Statistics
Summary Statistics for any numerical column
Count occurrences of each record
Correlation for numeric columns
Generate A Matrix for using PC and LDA
Perform LDA Linear Discriminant Analysis
Draw ROC plot on "Perform LDA" output
Compute q-values based on multiple simultaneous tests p-values
MINE - Maximal Information-based Nonparametric Exploration
GFF
Wavelet Analysis
Wavelet variance using Discrete Wavelet Transfoms
Graph/Display Data
Histogram of a numeric column
Scatterplot of two numeric columns
Bar chart for multiple columns
Plotting tool for multiple series and graph types
Boxplot of quality statistics
GMAJ Multiple Alignment Viewer
LAJ Pairwise Alignment Viewer
Build custom track for UCSC genome browser
VCF to MAF Custom Track for display at UCSC
Regional Variation
Assign weighted-average of the values of features overlapping an interval
Filter nucleotides based on quality scores
Mask CpG/non-CpG sites from MAF file
Fetch Indels from pairwise alignments
Fetch Indels from 3-way alignments
Estimate Indel Rates for 3-way alignments
Fetch substitutions from pairwise alignments
Estimate substitution rates for non-coding regions
Extract Orthologous Microsatellites from pair-wise alignments
Estimate microsatellite mutability by specified attributes
Delete Overlapping Indels from a chromosome indels file
Compute Motif Frequencies in indel flanking regions
Categorize Elements satisfying criteria
Draw Stacked Bar Plots for different categories and different criteria
Multiple regression
Multivariate Analysis
Evolution
Branch Lengths Estimation
dN/dS Ratio Estimation
Mutate Codons with SNPs
aaChanges amino-acid changes caused by a set of SNPs
phyloP interspecies conservation scores
Motif Tools
MEME - Multiple Em for Motif Elicitation
FIMO - Find Individual Motif Occurrences
Sequence Logo generator for fasta (eg Clustal alignments)
Multiple Alignments
ClustalW multiple sequence alignment program for DNA or proteins
Metagenomic analyses
FASTA manipulation
Concatenate FASTA alignment by species
FASTA-to-Tabular converter
Tabular-to-FASTA converts tabular file to FASTA format
FASTA Width formatter
RNA/DNA converter
Collapse sequences
NCBI BLAST+
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s)
NCBI BLAST+ blastp Search protein database with protein query sequence(s)
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s)
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s)
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s)
BLAST XML to tabular Convert BLAST XML output to tabular
NGS: QC and manipulation
FastQC: fastq/sam/bam
Fastqc: Fastqc QC using FastQC from Babraham
Illumina fastq
FASTQ Groomer convert between various FASTQ quality formats
FASTQ splitter on joined paired end reads
FASTQ joiner on paired end reads
Roche-454 data
AB-SOLiD data
Convert SOLiD output to fastq
Generic FASTQ manipulation
Filter FASTQ reads by quality score and length
FASTQ Trimmer by column
FASTQ Quality Trimmer by sliding window
FASTQ Masker by quality score
FASTQ interlacer on paired end reads
FASTQ de-interlacer on paired end reads
Manipulate FASTQ reads on various attributes
FASTQ to FASTA converter
FASTQ to Tabular converter
Tabular to FASTQ converter
FASTX-Toolkit for FASTQ data
Quality format converter (ASCII-Numeric)
FASTQ to FASTA converter
Clip adapter sequences
Collapse sequences
NGS: Picard (beta)
NGS: Mapping
Lastz map short reads against reference sequence
Lastz paired reads map short paired reads against reference sequence
Megablast compare short reads against htgs, nt, and wgs databases
Map with PerM for SOLiD and Illumina
NGS: Indel Analysis
Filter Indels for SAM
Extract indels from SAM
Indel Analysis Table for combining indel interval data
NGS: RNA Analysis
RNA-seq
Tophat for Illumina Find splice junctions using RNA-seq data
Tophat for SOLiD Find splice junctions using RNA-seq data
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments
Cuffdiff find significant changes in transcript expression, splicing, and promoter use
Filtering
Filter Combined Transcripts using tracking file
NGS: SAM Tools
Filter SAM on bitwise flag values
Convert SAM to interval
SAM-to-BAM converts SAM format to BAM format
BAM-to-SAM converts BAM format to SAM format
Merge BAM Files merges BAM files together
MPileup SNP and indel caller
Generate pileup from BAM dataset
Filter pileup on coverage and SNPs
Pileup-to-Interval condenses pileup format into ranges of bases
flagstat provides simple stats on BAM files
rmdup remove PCR duplicates
NGS: GATK Tools (beta)
Alignment Utilities
Depth of Coverage on BAM files
Print Reads from BAM files
Realignment
Realigner Target Creator for use in local realignment
Indel Realigner - perform local realignment
Base Recalibration
Count Covariates on BAM files
Table Recalibration on BAM files
Analyze Covariates - draw plots
Genotyping
Unified Genotyper SNP and indel caller
Annotation
Filtration
Variant Filtration on VCF files
Select Variants from VCF files
Variant Quality Score Recalibration
Variant Utilities
NGS: Peak Calling
MACS Model-based Analysis of ChIP-Seq
SICER Statistical approach for the Identification of ChIP-Enriched Regions
CCAT Control-based ChIP-seq Analysis Tool
GeneTrack indexer on a BED file
Peak predictor on GeneTrack index
NGS: Simulation
Simulate Illumina runs
SNP/WGA: Data; Filters
Data: Import and upload
Upload File from your computer
Access Libraries stored locally
Data: Filter and Clean
Clean genotypes: filter markers, subjects
Subset markers: region or rs list
LD Independent: filter high LD pairs - decrease redundancy
Simulate
Null phenotypes for testing
Null genotypes for testing
SNP/WGA: QC; LD; Plots
QC; Eigenstrat
QC reports: Marker and Subject measures
Eigensoft: PCA Ancestry using SNP
LD; Manhattan/QQ; GRR
LD plots: and comparisons with HapMap data
Manhattan/QQ: Plots for WGA P values
GRR: Pairwise Allele Sharing
SNP/WGA: Statistical Models
Case Control: for unrelated subjects
Transmission Distortion: for family data
Linear Models: for genotype data
Manhattan/QQ: Plots for WGA P values
Human Genome Variation
aaChanges amino-acid changes caused by a set of SNPs
phyloP interspecies conservation scores
SIFT predictions of functional sites
g:Profiler tools for functional profiling of gene lists
DAVID functional annotation for a list of genes
CTD analysis of chemicals, diseases, or genes
FunDO human genes associated with disease terms
snpFreq significant SNPs in case-control data
LD linkage disequilibrium and tag SNPs
PASS significant transcription factor binding sites from ChIP data
GPASS significant single-SNP associations in case-control studies
BEAM significant single- and multi-locus SNP associations in case-control studies
LPS LASSO-Patternsearch algorithm
HVIS visualization of genomic data with the Hilbert curve
Call SNPS with Freebayes Bayesian genetic variant detector
Convert CG MasterVar file to pgSnp format
Genome Diversity
Extract primers for selected SNPs
Select a specified number of SNPs
Specify a set of restriction enzymes
Extract DNA flanking chosen SNPs
VCF Tools
Intersect Generate the intersection of two VCF files
Annotate a VCF file (dbSNP, hapmap)
Filter a VCF file
Extract reads from a specified region