SNP/WGA: Data; Filters
Data: Import and upload
Upload File from your computer
Access Libraries stored locally
HapMapMart HapMap Biomart
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
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
Sanitize; replace phenotype data: from messy phenotype data
Normalize and QC Tools
Normalize Microarrays - rma,vsn..etc.
QC using arrayQualityMetrics
Statistical Models
One way anova: on Expression levels
Get Data
Upload File from your computer
UCSC Main table browser
UCSC Test table browser
UCSC Archaea table browser
BX main browser
BioMart Central server
BioMart Test server
GrameneMart Central server
Flymine server
Flymine test server
modMine server
Ratmine server
Wormbase server
Wormbase 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
UCSC bigbed converters
ENCODE Tools
Gencode Partition an interval file
Lift-Over
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 on ambiguities in polymorphism datasets
Filter and Sort
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
Wiggle-to-Interval converter
Extract Features
Gene BED To Exon/Intron/Codon BED expander
Extract features from GFF file
Fetch Sequences
Fetch Alignments
Split MAF blocks by Species
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
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
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
Boxplot of quality statistics
GMAJ Multiple Alignment Viewer
LAJ Pairwise Alignment Viewer
Build custom track for UCSC genome browser
Regional Variation
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
Multivariate Analysis
Evolution
Branch Lengths Estimation
Neighbor Joining Tree Builder
dN/dS Ratio Estimation
Mutate Codons with SNPs
Amino-acid changes caused by a set of SNPs
Add scores for interspecies conservation at each SNPs
Metagenomic analyses
FASTA manipulation
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
Illumina data
FASTQ Groomer convert between various FASTQ quality formats
FASTQ splitter on joined paired end reads
FASTQ joiner on paired end reads
FASTQ Summary Statistics by column
Roche-454 data
Combine FASTA and QUAL into FASTQ
AB-SOLiD data
Convert SOLiD output to fastq
Compute quality statistics for SOLiD data
Draw quality score boxplot for SOLiD data
Generic FASTQ manipulation
Filter FASTQ reads by quality score and length
FASTQ Trimmer by column
Manipulate FASTQ reads on various attributes
FASTQ to FASTA converter
FASTQ to Tabular converter
Tabular to FASTQ converter
NGS: Mapping
NGS: SAM Tools
Filter SAM on bitwise flag values
Convert SAM to interval
Merge BAM Files merges BAM files together
Filter pileup on coverage and SNPs
Pileup-to-Interval condenses pileup format into ranges of bases
NGS: Peak Calling
MACS Model-based Analysis of ChIP-Seq
GeneTrack indexer on a BED file
Peak predictor on GeneTrack index