Get Data
Upload File from your computer
UCSC Main table browser
UCSC Test table browser
UCSC Archaea table browser
Get Microbial Data
BioMart Central server
BioMart Test server
GrameneMart Central server
Wormbase server
Wormbase test server
Flymine server
Flymine test server
EuPathDB server
EncodeDB at NHGRI
EpiGRAPH server
EpiGRAPH test server
HbVar Human Hemoglobin Variants and Thalassemias
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 query
Compute an expression on every row
Concatenate queries tail-to-head
Cut columns from a table
Merge Columns together
Convert delimiters to TAB
Create single interval as a new query
Change Case of selected columns
Paste two files side by side
Remove beginning of a file
Select first lines from a Query
Select last lines from a Query
Trim leading or trailing characters
Filter and Sort
Filter data on any column using simple expressions
Sort data in ascending or descending order
Select lines that match an expression
Join, Subtract and Group
Join two Queries side by side on a specified field
Compare two Queries to find common or distinct rows
Subtract Whole Query from another query
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 converts FASTA file to tabular format
GFF-to-BED converter
LAV to BED Converts a LAV formatted file to BED format
Maf to BED Converts a MAF formated file to the BED format
MAF to Interval Converts a MAF formatted file to the Interval format
MAF to FASTA Converts a MAF formated file to FASTA format
Tabular-to-FASTA converts tabular file to FASTA format
FASTQ to FASTA 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
Filter MAF blocks by Size
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 queries
Subtract the intervals of two queries
Merge the overlapping intervals of a query
Concatenate two queries into one query
Base Coverage of all intervals
Coverage of a set of intervals on second set of intervals
Complement intervals of a query
Cluster the intervals of a query
Join the intervals of two queries side-by-side
Get flanks returns flanking region/s for every gene
Fetch closest feature for every interval
Profile Annotations for a set of genomic intervals
Statistics
Summary Statistics for any numerical column
Count occurrences of each record
Correlation for numeric columns
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
GMAJ Multiple Alignment Viewer
LAJ Pairwise Alignment Viewer
Build custom track for UCSC genome browser
Visualize BED file - creates a visualization from a bed file
Peak predictor - generates peak predictions from an index file
Regional Variation
Make windows
Feature coverage
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
Multiple regression
Evolution
Branch Lengths Estimation
Neighbor Joining Tree Builder
dN/dS Ratio Estimation
Mutate Codons with SNPs
Metagenomic analyses
FASTA manipulation
Compute sequence length
Filter sequences by length
Concatenate FASTA alignment by species
FASTA-to-Tabular converts FASTA file to tabular format
Tabular-to-FASTA converts tabular file to FASTA format
FASTA Width formatter
RNA/DNA converter
Collapse sequences
NGS: QC and manipulation
NGS: Mapping
Map with Bowtie
Map with BWA
Megablast compare short reads against nt and wgs databases
Parse blast XML output
NGS: SAM Tools
Filter SAM on bitwise flag values
Convert SAM to interval
SAM-to-BAM converts SAM format to BAM format
Merge BAM Files merges BAM files together
Generate pileup from BAM dataset
Filter pileup on coverage and SNPs
Pileup-to-Interval condenses pileup format into ranges of bases
Rgenetics: Data; Filter
Import Rgenetics data from system library
Upload File from your computer
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
Rgenetics: Plots; Models
QC reports: Marker and Subject measures
Eigensoft: PCA Ancestry using SNP
LD plots: and comparisons with HapMap data
QQ Plots: for p values from an analysis
GRR: Pairwise Allele Sharing
Statistical Models
Linear Models: for genotype data
Case Control: for unrelated subjects
Transmission Distortion: for family data
Rexpression: Gene Expression
External Data Sources
Get GEO data: for a GDS id
Get ArrayExpress data: use an ArrayExpress id
Data Subset/Clean Tools
Subset Expression experiments with BioConductor simpleaffy
Clean nasty metacharacters: from messy phenotype data
Normalize and QC Tools
Normalize Microarrays - rma,vsn..etc.
QC using arrayQualityMetrics
Statistical Models
One way anova: on Expression levels