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Pipeline & Protocol
Toolkit
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C
C++
GPU
Hadoop
Java
Perl
Python2
Python3
R
Spark
Platform
Linux/Unix
MAC OS X
Windows
User Interface
Desktop GUI
Terminal Command Line
Webpage
Input Data
BAM
FASTA
FASTQ
SAM
VCF
Category
Base calling
Read quality control
Error correction
Duplicate read removal
Adapter trimming
MinION real-time analysis
Read clustering
Read alignment
Read alignment visualization
SNP detection
De novo mutation detection
CNV detection
Somatic CNA detection
Microsatellite detection
Transposon detection
Numt insertion detection
NAHR detection
Structural variant detection
Variant aggregation/summarization
Variant recalibration
Variant visualization
Variant effect prediction
Splicing defect prediction
Driver mutation prioritization
Interpretation
Genetic ancestry
Identity by descent
Pedigree drawing
Pedigree reconstruction
SNP/SNV annotation
Retroviral vector integration site detection
CNV annotation
Ancient DNA analysis
Virus detection
Haplotype assembly
Tumor purity and heterogeneity estimation
Read simulation
Variant simulation
DNA sequence data compression
Data file formats
Other tools
LIMS
Utilities
Fetal CNV detection
Non-coding driver mutation detection
Mitochondrial DNA data processing
Telomere content estimation
Index construction
Multilocus sequence typing
Depth of coverage
Quality control
CNV detection
Somatic CNA detection
HLA typing
Allelic imbalance detection
Autozygosity mapping
Variant prioritization
De novo mutation detection
SNP/SNV annotation
Variant visualization
Interpretation
Internal tandem duplication detection
Genome assembly
Reference-assisted assembly
Assembly scaffolding
Assembly reconciliation
Assembly evaluation
Assembly visualization
Gap closing
Assembly circularization
Transposon annotation
Other tools
Multilocus sequence typing
Genome profiling
Experimental design
Quality control
Spliced read alignment
De novo transcriptome assembly
Assembly evaluation
Read realignment
Read count
Transcript quantification
Transposable element expression
Normalization/differential expression
Alternative splicing
Gene fusion detection
Driver gene fusion prediction
Gene prediction
Sex-linked gene detection
Transcriptome annotation
Variant detection
Allele-specific expression
Circular RNA detection
RNA editing
HLA genotyping
Alternative polyadenylation
Co-expression network analysis
Gene expression clustering
Gene set analysis
Time course
Differential meta-analysis
Data visualization
Allopolyploidy analysis
Read simulation
Splicing QTL detection
RBP motif enrichment
Other tools
Operon structure prediction
Experimental design
Quality control
Peak calling
Peak annotation
Normalization
Tag density plot visualization
Differential peak calling
Motif discovery
Nucleosome positioning
Allele-specific binding
Chromatin segmentation
Target gene detection
Tumor heterogeneity deconvolution
Data visualization
Interpretation
Read simulation
Other tools
tRNA-derived RNA annotation
miRNA mappers
ncRNA identification
IsomiR detection
ncRNA-related SNPs
Software pipelines
miRNA prioritization
Experimental design
Quality control
Read alignment
Methylation scoring
Differentially methylated region detection
Quantitative score assessment
Methylation annotation
SNP detection
Allele-specific DNA methylation detection
Transcription factor binding prediction
Tumor purity deconvolution
Data visualization
Interpretation
Read simulation
Sequence contamination detection
Ribosomal gene prediction
Protein database search
Quality control
Assembly
Fragment recruitment
Taxonomy-dependent
Taxonomy-independent
Differential abundant feature detection
Gene prediction
CRISPR detection
Variant detection
Functional annotation
Protein sequence reconstruction
Interpretation
Data visualization
Viral annotation
Read simulation
rRNA databases
Pipelines
Unclassified tools
Plasmid detection
Microbial strain identification
ORF detection
16S rRNA reconstruction
RNA-BSseq
Experimental design
Probe design
Chimera detection
Denoising
Homology-based taxonomic classification
Prediction-based taxonomic classification
Correlation inference
Functional profile prediction
RNA motifs discovery
miRNA target identification
Pipelines
Read alignment
Quality control
Contact matrix generation
Contact matrix normalization
Peak calling
Domain calling
Centromere calling
Data interpretation
Differential interactions analysis
Differential loops analysis
3D structure prediction
Assembly scaffolding
Data integration
Pipelines
Hybridization capture
Amplicon sequencing analysis
GBS analysis
Demultiplexing
SNP detection
Indel detection
Transposon detection
Population genetic analysis
Haplotype frequency estimation
Genetic mapping
Viral population reconstruction
Other tools
RAD-seq analysis
Rep-seq analysis
Strand-seq analysis
Deep mutational scanning analysis
GRO-seq analysis
Tn-seq analysis
CAGE analysis
scRNA-seq analysis
DGE analysis
dRNA-seq analysis
RNA structurome analysis
De novo ChIP-seq analysis
DNase-seq analysis
Nucleosome positionning analysis
Ribo-seq analysis
ChIP-exo analysis
HT-SELEX analysis
Degradome-seq analysis
MeDIP-seq analysis
MethylCap-seq analysis
oxBS/TAB/fCAB/CAB-seq
Metatranscriptomic sequencing analysis
CRISPR/Cas9 screen analysis
Drop-seq analysis
3D structure prediction
Nucleosome positionning analysis
Single-cell assemblers
3C-seq analysis
4C-seq analysis
3D structure prediction
RIP-seq analysis
Microarray interconversion
Image analysis
Noise reduction
Normalization
Segmentation
CNV detection
Somatic CNA detection
Copy number and gene expression data integration
Interpretation
Oligonucleotide design
Data import
LIMS
Chromothripsis-like pattern detection
ChIP-on-chip
Tumor purity
Data preprocessing
Differential expression
Clustering
Classification
Alternative splicing
Time course
Data visualization
Meta-analysis
Venn diagrams
MicroRNA microarray
Antibody microarray
Peptide microarray
Reverse phase protein array
Tissue microarray
Quality control
RNA identification
2D gel image analysis
Glycosylation identification
In silico analysis
Data conversion
Mass bias correction
Peak detection
Peak alignment
Phosphorylation site assignment
PTM identification
Database search
Amino acid mutation identification
De novo peptide sequencing
Protein inference
Peptide assignment validation
Hydrogen-deuterium exchange
Label-free protein quantification
Isobaric labeling protein quantification
Isotopic labeling protein quantitation
Differential protein expression
Data simulation
Cross-linked peptide identification
Interpretation
Spectral libraries
LIMS
Data preprocessing
Peptide selection
Downstream analysis
MS-based metaproteomics
Proteogenomics
Data preprocessing
Metabolite identification
Lipid identification
In silico fragmentation
Interpretation
Other tools
MS-based targeted metabolomics
Spectra visualisation
Peak picking
Resonance assignment
NOE assignment
Protein dynamics
NMR simulation
Chemical shift prediction
Data processing
Metabolite identification
Chemometric analysis
NMR spectra
Single-cell qPCR
Conventional primers
Degenerate primers
Multiplex primers
Polyploid primers
Mutagenic primers
Primer quality
Reference genes
Data analysis
Primer databases
Data standards
Other tools
dPCR
Data preprocessing
Normalization
Quality control
Cell population identification
Software pipelines
Data repositories
Utilities
Phylogenetic programs
Analytical pipelines
Data standards
Education
Data visualization
Mass cytometry
Image segmentation
Multiview deconvolution
Image-analysis libraries
FISH
cryo-EM
Neuron tracing
Biological network reconstruction
Scanning force microscopy
Image acquisition
Cell tracking
Particle tracking
Mass spectrometry imaging
Subcellular protein distribution
Super-resolution imaging
High-throughput screening
Neurite growth
Image data
Data management and annotation
Image cytometry
Thermal shift assay
Small-angle scattering
Optical tomography
Structure orientation
Brain connectomics
SPIM
Scratch assay
Kinematics analysis
Animal behavior tracking
Analytical pipelines
Base callers
Trace editors
Aligners
Genome assemblers
Variant detection
Unclassified tools
DNA fingerprinting
Optical mapping
nCounter System
Circular dichroism spectroscopy
Genome data
Gene data
Annotation pipeline
Gene prioritization
Genome visualization
Promoter prediction
Enhancer prediction
Motif discovery
Motif enrichment
Motif scanning
Motif comparison
Functional TFBS identification
Genomic region enrichment
Cis-regulatory DNA element data
Super-enhancer data
SnoRNA gene prediction
Impact of variants on miRNAs
Genomic interval association
Genome assembly data
Taxonomy identification
Indel extraction
Mutational signature identification
rSNP prediction
tRNA gene prediction
Protein-coding gene prediction
Frameshift prediction
Absent word detection
CpG island prediction
Genomic island prediction
Chloroplast DNA data
Mitochondrial DNA data
Integron data
CRISPR prediction
miRNA precursor prediction
Intronless gene data
DNA triplex prediction
DNA triplex data
Gene visualization
Operon data
Data warehousing systems
Translational research platforms
DNase I hypersensitive-site prediction
Transposable element prediction
Transposable element data
Tandem repeat prediction
Tandem repeat data
Insertion sequence prediction
Prophage prediction
Cooperative transcription factor prediction
Multi-locus sequence typing data
Cis-regulatory module prediction
Transcription factor binding site prediction
Phylogenetic inference
Phylogenetic tree visualization
Phylogenetic network construction
Discrete character evolution
Ancestral sequence reconstruction
Community phylogenetics
Cophylogeny reconstruction
Reconciliation visualization
Phylogeographic reconstruction
Supertree construction
Tumor progression
Viral sequence classification
Phylogenetic congruence
Tree comparison
Haplogroup prediction
Model selection
Workflows/pipelines
Missing data prediction
Tip dating
Comparative analysis
Ancestral genome reconstruction
Other tools
Sequence alignment visualization
Ultraconserved sequence data
Multiple sequence alignment quality control
Whole genome alignment
Pairwise sequence alignment
Multiple sequence alignment
Maximal exact match detection
Gene structure comparison data
Pan-genome analysis
Gene orthology prediction
Sequence homology search
Sequence logo generation
Metagenomic data
Comparative genome visualization
Gene ortholog data
Synteny detection
Fractionation
Comparative genome data
Natural selection
Population structure
backwards
forwards
Haplotype phasing
Geographic assignment
Haplotype network construction
Familial aggregation analysis
Cluster analysis and visualization
Reverse ecology
TCGA data access
Rare and low-frequency variation data
Variant-disease association databases
Clinical genomic databases
Disease-specific variation databases
Locus-specific variation databases
Copy number alteration data
Mitochondrial variation databases
National & ethnic variation databases
Non-human variation databases
CRs/fusion genes
Gene fusion visualization
Standards & guidelines
Variation ontologies
CRISPR/Cas9
TALENs
ZFNs
Meganucleases
Educational websites
Personal genomics
Metabolic pathways
Deprecated resources
Sexual reproduction
DNA methylation
Histone modifications
Nucleosome positioning
Genome structure
Chromatin-state detection
DNA modification data
DNA methylation deconvolution
Pseudouridine site prediction
RNA methylation data
RNA methylation prediction
miRNA data
LncRNA data
LncRNA interaction data
LncRNA disease association data
LncRNA-disease association prediction
ta-siRNA data
Natural antisense transcript data
Bacterial sRNA target prediction
Bacterial sRNA data
CircRNA data
shRNA data
tRF data
SnoRNA data
tmRNA data
piRNA data
Translated mRNA data
Translation initiation site prediction
Ab initio gene prediction
Gene set analysis
Topology-based pathway analysis
Microarray repositories
Gene expression data
Gene co-expression data
Gene co-expression prediction
miRNA target prediction
miRNA target data
Alternative splicing data
Alternative splicing annotation
RBP-target interaction data
RBP-target interaction prediction
Cis-regulatory RNA element data
Cis-regulatory RNA element prediction
Polyadenylation data
Polyadenylation prediction
RNA editing data
RNA editing prediction
Coding and noncoding region discrimination
Riboswitch detection
EST data
Translational efficiency prediction
Translation initiation site data
Semantic similarity measurement
siRNA data
tRNA data
IsomiR data
Mature miRNA sequence prediction
Prognostic signature prediction
miRNA enrichment
Differential co-expression
Prognostic biomarker identification
Heatmap generation
Competing endogenous RNA
miRNA name translation
Periodicity detection
Circadian gene expression data
High-throughput RNAi screening
RNAi reagent design
RNAi phenotypic data
Unclassified tools
Sequence data
Expression data
Proteome data
Transcription factor data
Amino acid repeat prediction
Amino acid repeat data
Subcellular localization prediction
Subcellular localization data
Secretome data
Extracellular matrix data
Annotation
Function prediction
Substrate cleavage prediction
Enzyme data
T3S effector prediction
Viral structural protein prediction
Leucine-rich nuclear export signal prediction
Multitasking protein data
Redundancy reduction
Mitochondrial data
Chloroplast data
Feature visualization
Domain prediction
SDS prediction
Coreceptor usage prediction
Mutated data
Telomerase data
SLiM prediction
LCR prediction
RNA-binding protein data
Transcriptional regulatory module prediction
Peptide clustering
Protein clustering
Q/N rich prion-like domain prediction
PseAA composition
pKa prediction
Isoelectric point prediction
Other tools
Nuclear receptor data
Pairwise sequence alignment
Multiple sequence alignment
Multiple domain alignment
Sequence alignment visualization
Sequence homology search
Family data
Phosphorylation site prediction
Phosphorylation site data
Dephosphorylation site prediction
Mutation impact on phosphorylation
Ubiquitination site prediction
Ubiquitination site data
S-nitrosylation site prediction
S-nitrosylation site data
Glycosylation site prediction
Glycosylation site data
Prenylation site prediction
Prenylation site data
N-myristoylation site prediction
N-myristoylation site data
Succinylation site prediction
Succinylation site data
Phosphoglycerylation site prediction
Phosphoglycerylation site data
Palmitoylation site prediction
Palmitoylation site data
Acetylation site prediction
Acetylation site data
Pupylation site prediction
Pupylation site data
S-sulfenylation site prediction
Methylation site prediction
GPI anchor attachment prediction
SUMOylation site prediction
Crosstalk prediction
Hydroxylation site prediction
Tyrosine nitration site prediction
Oxidative modification data
S-glutathionylation site data
ADP-ribosylation site data
Other tools
Metabolite enrichment analysis
Transcriptomic and metabolomic data integration
Glycomics
Metabolite libraries
Spectral libraries
Biodegradation
Constraint based methods
13C-fluxomics
Differential network
Gene network data
Gene network inference
Protein-protein interaction data
Protein-protein interaction prediction
Metabolic network data
Metabolic network analysis
Gene regulatory network inference
Gene regulatory network data
Host-pathogen interaction data
Host-pathogen interaction inference
Signaling pathways
Phosphorylation network data
Kinase-substrate relationship inference
Module extraction
Network alignment
Subnetwork search
Network motif detection
Network simulation
Driver pathway detection
Genotype network inference
Network visualization
Interaction confidence scoring
Intercellular signaling data
Pathway crosstalk network prediction
Signaling pathway crosstalk data
Synthetic lethality prediction
Protein complex prediction
De novo network enrichment
Isoform-level network modeling
Network analysis
Cell cycle
Cell deaths
14-3-3-binding phosphosite prediction
Centrality exploration
Ubiquitin-mediated signalling
Multi-omic data integration
miRNA regulatory modules inference
Deregulated subnetwork detection
Protein similarity network generation
Other tools
Gap filling
Quality control
Genotype imputation
Summary statistics
Single SNP association
CNV association
Fine mapping
Region-based association
Association mapping
Rare variant association
Joint association
Complex trait prediction
Epistasis detection
Linkage disequilibrium assessment
Haplotype association
IBD segment detection
Pathway analysis
SNP prioritization
Meta-analysis
Data visualization
Simulation
Genetic association data
Other tools
Linkage analysis
QTL mapping
eQTL mapping
EWAS
mGWAS
PheWAS
Phenomics
Chemical enrichment analysis
Protein-protein interaction modulators
Natural products
Chemical translation
Ligand-based
Structure-based
Pocket detection
Protein-ligand docking
Protein-protein docking
Drug targets
GPCR-ligand interactions
Protein-peptide docking
DDIs
RNA-ligand interactions
Combinatorial libraries
Drug metabolism
Drug repositioning
Drug sensitivity
Drug resistance
Adverse drug reactions
Drug pathways
Network pharmacology
Pharmacogenetics
Toxicogenomics
Dose-response
Quorum sensing peptide data
Peptide structure prediction
Antimicrobial peptide data
Neuropeptide data
Antiviral peptide data
Cell penetrating peptide data
Biopanning data
Secondary metabolite biosynthetic pathways
miRNA pharmacogenomics
QSAR toxicity predictions
Molecule editors
Molecule viewers
Workflow systems
Binding affinity prediction
Drug combination analysis
GPCR-ligand docking
Connectivity mapping
Other tools
Compound similarity visualization
Chemical-transporter interaction data
RNA design
Translation efficiency
Gene design
Essential genes
Plasmid collections
LIMS
Circuit design
Model selection
Cell-based modeling
Spatial stochastic simulation
Population dynamics
Primer design
Model repositories
Biological part libraries
DNA design
Strain design
Thermodynamics
Structure conservation prediction
Repetitive element prediction
Volume calculation
Allosteric site prediction
Co-evolving residue prediction
Multiple structure alignment
Shape prediction
Pseudoknot prediction
Secondary structure visualization
Protein structures
riboSNitch prediction
Structure alignment
Disorder prediction
Structure validation
Hot spot prediction
Contact map prediction
Hydration prediction
Stability change prediction
Coiled-coil domain prediction
Knot prediction
Internal symmetry prediction
Circular permutation prediction
Dynamics prediction
Domain movement prediction
Transmembrane helix prediction
Transporters
Receptors
OMPs
Transmembrane β-barrel prediction
Membrane simulation
Unclassified biomolecular structure tools
Channel detection
Aggregation prediction
Protein structure comparison
Disulfide bonding prediction
Solubility prediction
Protein-metal site prediction
Protein-DNA interaction prediction
Protein-nucleic acid docking
Workflow systems
Pairwise structure alignment
R-loop forming sequence prediction
R-loop forming sequence data
Structural motif detection
Protein-protein interface prediction
Tunnel detection
Cavity detection
Sequence-structure pattern search
Homo-oligomer structure prediction
Loop modeling
Protein structural motif detection
RNA-RNA interaction prediction
Synthetic fusion protein design
Protein flexibility prediction
Protein structure manipulation
Protein dynamic domain identification
NMR structure refinement data
Protein binding-site similarity detection
Protein dihedral angle prediction
Protein design
Protein structure decoy generation
Protein fold recognition
Protein structure refinement
Protein-protein structure prediction
Solubility mutagenesis prediction
Conformational diversity data
Protein-surface structure prediction
Solvent accessibility prediction
Functional site prediction
Structure refinement
Structural domain prediction
Protein crystallization prediction
Protein quality assessment
Visualization
Certain infectious and parasitic diseases
Neoplasms
Diseases of the blood and blood-forming organs
Endocrine, nutritional & metabolic diseases
Mental and behavioural disorders
Eye and adnexa
Diseases of the circulatory system
Nervous system
Musculoskeletal system & connective tissue
Perinatal period
Congenital malformations, deformations & CA
Ageing
Disease similarity identification
Disease ontologies
Comorbidity risks
Tissue banks
Antibody structure
B-cell epitopes
T-cell epitopes
Innate immunity
Allergen prediction
Other unclassified tools
Epitope selection
Proteasomal cleavage
TAP prediction
Autoantigen data
Text mining
Search
CloudPhylo
Phylogeny reconstruction on large-scale datasets
Tool Type:
Application
Technologies:
Java
,
Spark
Download Count: 235