Galaxy
Analyze Data
Workflow
Visualize
Create Visualization
Interactive Environments
Saved Visualizations
Shared Data
Data Libraries
Histories
Workflows
Visualizations
Pages
Help
Support
Search
Mailing Lists
Videos
Wiki
How to Cite Galaxy
Interactive Tours
Login or Register
Login
Register
Using 0 bytes
Tools
Get Data
Upload File
from your computer
UCSC Main
table browser
EBI SRA
ENA SRA
Basespace
getting data
GeNeo Toolbox
Variant Calling and Filtering
CCCP:
Run Consensus Caller Cross-Platform pipeline
Somatic SNV Filter:
Select somatic calls made by the CCCP pipeline
dbSNP Filter:
Select SNVs that are not in dbSNP
RNA Coverage Filter:
Select SNVs with specified RNA coverage
VCF Generator:
Convert list of SNVs in CCCP output format to VCF
Summary Report Generator:
Collect statistics from a CCCP log file
Variant Validation
Primer Designer:
Design primers for AmpliSeq AccessArray or Sanger resequencing of given SNVs
AA Genotype Caller:
Demultiplex AmpliSeq AccessArray reads and call genotypes for target SNVs
Alignment Extractor:
Generate reduced reference and bam files to visualize reads in IGV
MitoMatch
Check for matching mitochondrial haplogroups of sequenced samples
Neoepitope Prediction
Seq2HLA:
Predict HLA class I and II alleles using Illumina paired-end RNA-seq reads
Neoepitope Finder:
Predict neoepitopes for SNVs called using CCCP
IC50 Filter:
Select neoepitopes based on predicted IC50
DAI Filter:
Select neoepitopes based on Differential Agretopic Index
Transcriptomics
RNA-Seq Analysis
IsoEM2
Infers isoform and gene expression levels with bootstrap based confidence intervals from either sense, antisense, or non-stranded RNA-Seq data
Aggregator
Aggregates IsoEM2 output files and generates PCA plots
IsoDE2
Computes differentially expressed isoforms and genes based on bootstrap samples generated by IsoEM2
Fold Change Filter
Filters IsoDE2 output based on fold change
Metatranscriptomics
Pathway Activity
EMPathways
Quantifies metabolic pathway activity levels from metatranscriptomic data by Expectation-Maximization
DE
Performs differential pathway activity analysis using pathway expressions generated from the EMPathways pipeline
Mitogenomics
mtDNA Forensics
MitoID
Infer the mitochondrial haplogroup from sequencing data
Mitogenome Assembly
Get Sequence
from NCBI GenBank
SMART
- Statistical Mitogenome Assembly with Repeats
SMART2:
Multi-Sample Statistical Mitogenome Assembly with Repeats
Immunopeptidomics
MS-GF+ Tools
MS-GF+ Percolator
FDR filter
Viral Genomics
Viral Genomic Assembly
CliqueSNV
is a novel reference-based method for reconstruction of viral variants from NGS data.
Search did not match any tools.
Workflows
All workflows
History
loading...