Analyze Data
Workflow
Shared Data
Data Libraries
Histories
Workflows
Visualizations
Pages
Visualization
New Track Browser
Saved Visualizations
Interactive Environments
Help
Support
Search
Mailing Lists
Videos
Wiki
How to Cite Galaxy
Interactive Tours
Login or Register
Login
Register
Galaxy / CropGalaxy
Using 0 bytes
Tools
Get Data
RAVE
- Rapid Allelic Variant Extractor
Decompress an archive
in zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2 format
Upload File
from your computer
Gigwa
: SNP filtering
APPGCC
RShiny tool
RiceGalaxy: SNP Data Tools
FGSEA-2
- fast preranked gene set enrichment analysis
Find-gene-by-terms
Find gene(s) using a single or list of text terms/phrases
Find-seq
Align your nucleotide sequences to rice variety-representative genomes
Get-contig-names
Extract contig / scaffold / chromosome / gene names from representative rice genomes
Get-genes-by-region(s)-IDs v2
Retrieve list of genes within specified region of rice genomes
Get-subseq
Extract sequence for your gene IDs (entire or region) from rice genome or multiFASTA file
Liftover_via_SNP
Lift a large chromosome region flanked by 2 SNPs from one genome to another
Blat Alignment Filter
Stringent filtering of alignment results (psl v3, from blat)
RiceGalaxy: GEMMA
Convert ped files to binary
Compute Principal Components
Compute Kinship from Genotype
Add Pheno to Fam File
Association with Linear Model
Mixed Linear Model
Plot Results
Make Manhattan and QQ plots
RiceGalaxy: Pathology and Disease Tools
Pathotype Identifier
for rice datasets
Plink Data Tools
Filter
Genotypes
LD prune
dataset
LD clumping and annotation
LD-based result clumping
Compute Distance Matrix
from genotypes
Compute Allele Frequencies
across genotypes
Filter
Genotypes in pbed format
LD prune
dataset using pbed
GEA-R Tools
GEA-R:AMMI-SREG
R script in Galaxy
Factorial Regression:GEA-R
R script in Galaxy
PLS:GEA-R
R script in Galaxy
EIB: Genomic Selection
BLUP/BLUE
calculator (multiple traits)
Hapmap filter
Filter per SNPs based on user-specified criteria
Numeric matrix encoder
encodes genotypes to numeric
Sample Matching
compares samples between genotype and phenotype files
Parallel Genotype-Phenotype Matching
genotype and phenotype files
Parallel Genotype-Phenotype Matching
genotype and phenotype files
GEBV
calculator
Cross validation
within and across groups
K-fold Cross-validation
model training
Split datasets by grouping factor
Merge multiple GEBV results
Data Format Conversion
Make Bed Files
From composite data
Convert bed/bim/fam
to ped/map
Make VCF Files
From composite data
Convert Hapmap to Plink
genotype format
Convert Hapmap to VCF
genotype format
Convert Flapjack to VCF
genotype format
Convert genotyping data
converts various genotyping formats
Convert BLUP output
to be compatible with GEBV (sample matching)
Convert BLUP output
to be compatible with GEBV
Convert GEBV output
to be compatible with scatter plot
Generate membership file
in the same order as phenotype file
Create Grouping File
to be compatible with cross-validation
BCFTools
Get Standard statistics
from VCF
BCFTools filtering
Convert formats
Create Variant ID
from VCF
Extract QC annotations
from VCF
Marker Selection
sample SNPs
Take a random sample of SNPs from a file
Sample-based genome-wide LD
Estimate linkage disequilibrium decay with distance
Purity
marker selection from a HapMap file using Genetic Algorithm
Purity (beta)
supports VCF file format
Prune SNPs
on LD threshold (plink)
Convert VCF
to BED (plink)
Imputation
Naive imputation
using population mean or mode
Beagle
imputation
Impute2
imputation
makeNPUTEinputmatrix
Creat NPUTE input matrix from HapMap file.
NPUTE
Numerical Imputation
makeHMPfromNPUTEoutput
Creat Hapmap file from NPUTE output matrix.
Impute Validation
File Input
Change calls to missing
calls with a given rate.
OGHMA
encode
encode genotypes for further machine learning analysis
folds
create folds for classifiers evaluation through cross-validation
LASSO
predict phenotype using a LASSO approach
svm
predict phenotype using a SVM approach
randomForest
predict phenotype using a random forest approach
compute R2
compute R-squared value of a prediction vs true phenotype
evaluation
evaluate results of classifiers prediction
prediction
use machine learning model to predict phenotype from genotype
plot prediction
shows scatterplot of a prediction vs true phenotype
Cluster Analysis
Calculate Distance Matrix
from Genotype Data
SNPRelate GRM
calculator
Get Distance Matrix
from Genotype Data
Principal Component Analysis
Hybrid K-Means Clustering
K-Means Clustering
TASSEL: GWAS tools
Calculate Kinship
from Genotype Data
Run PCA
(Principal Component Analysis) on genetic data
Association using GLM
(General Linear Model)
Association using MLM
(Mixed Linear Model)
Text Manipulation
Add column
to an existing dataset
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
Line/Word/Character count
of a dataset
Secure Hash / Message Digest
on a dataset
Collection Operations
Unzip Collection
Zip Collection
Filter failed
datasets from a list
Flatten Collection
into a flat list of datasets
Merge Collections
into single list of datasets
Relabel List Identifiers
from contents of a file
Filter List
from contents of a file
Sort Collection
of list of 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
Filter GTF data by attribute values_list
Join, Subtract and Group
Join two Datasets
side by side on a specified field
Compare two Datasets
to find common or distinct rows
Group
data by a column and perform aggregate operation on other columns.
Uniqprimer
Uniqprimer
Design specific primers of sequences
Statistics
Summary Statistics
for any numerical column
Count
occurrences of each record
Graph/Display Data
Bar chart
for multiple columns
Boxplot
of quality statistics
VCF to MAF Custom Track
for display at UCSC
InTreeGreat
Display Newick tree
CircosJS
CircosJS Client to build interactive graphs in a circular layout
Highcharts scatter plot
using columns of a tabular file
Highcharts Bar Charts
displays values from columns of a tabular file
VCF intersect
VCF intersect
- VCF intersection
Pre-genotyping
Get Intertek Order form and HTPG Sample File
Get a list of Unique IDs (UIDs) in a text file
SimpleTracker
Generates sample IDs and plate layout for sample barcoding and collection
Post-genotyping
Intertek / Flapjack - SNP Sample File Processor
convert an HDF5 formatted genotype file into a Flapjack formatted genotype file
Intertek-Flapjack Converter
Extract txt files from Excel workbook
Convert csv file to txt format
Tools from Toolshed
RAVE
RAVE
- Rapid Allelic Variant Extractor
SNIPLAY
sNMF
Fast and efficient program for estimating individual ancestry coefficients
SnpEff
Predicts SNP effect from a genomic VCF file
Tassel
Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium
MLMM (GWAS analysis)
GWAS using Multi-Locus Mixed-Model (MLMM)
SnpSift Annotate
SNPs from dbSnp
SnpSift Intervals
Filter variants using intervals
SnpSift rmInfo
remove INFO field annotations
SnpSift Variant Type
Annotate with variant type
SnpSift CaseControl
Count samples are in 'case' and 'control' groups.
SnpSift Extract Fields
from a VCF file into a tabular file
SnpSift Filter
Filter variants using arbitrary expressions
SnpSift vcfCheck
basic checks for VCF specification compliance
FastME
Distance-based inference of phylogenetic trees
PLINK: MDS plot
IBS matrix / multi-dimensional scaling
Ped2Fasta
Convert PED file to Fasta File
Get VCF annotation statistics
Get annotation fromi a VCF file annotated by snpeff
SNP density
Calculate SNP densities along chromosome from a VCF input
PLINK: ped2bed
Convert ped to bed
HapmapToMLMMFiles
Converts a hapmap file into MLMM input files
Rooting
Midpoint rooting of newick tree
Get Haplotypes From Phased VCF
Get Haplotypes From Phased VCF
Check GWAS Inputs
Checks concordance between input files for GWAS analysis
Diversity by gene
Calculates various diversity indexes with EggLib
VCF to Hapmap
Convert VCF to Hapmap
VCFtools Filter
VCFtools Filter
VCFtools SlidingWindow
VCFtools SlidingWindow
VCFtools Stats
VCFtools Stats
Readseq
Convert various alignment formats
PLINK
Filter large VCF file
GOBII Tools
Flapjack to HDF5
convert a Flapjack formatted genotype file into HDF5
Transpose
transpose a file's contents
HapMap to Flapjack
convert a HapMap formatted file into a Flapjack formatted genotype file
Flapjack CreateProject
create a Flapjack project file from Flapjack formatted input files.
Flapjack Create Similarity Matrix
create a similarity matrix from a Flapjack formatted genotype file
Flapjack PedVerStats
run pedigree verification of F1s (known parents) analysis on a dataset
Flapjack Split By Sample
create a Flapjack project file from Flapjack formatted input files.
Flapjack MABCStats
run marker assisted backcrossing (MABC) analysis on a dataset
HDF5 to Flapjack
convert an HDF5 formatted genotype file into a Flapjack formatted genotype file
Visualization
Manhattan plot
Generate plots for use with GWAS pipelines
Search did not match any tools.
Workflows
All workflows
History
loading...