Name

Tool TypeApplication Framework Infrastructure Pipeline & Protocol Toolkit

TechesBASH C C++ GPU Hadoop Java Perl Python2 Python3 R Spark

PlatformLinux/Unix MAC OS X Windows

User InterfaceDesktop GUI Terminal Command Line Webpage

Input DataBAM FASTA FASTQ SAM VCF

CategoryBase 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

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• 高通量原位结构解析软件包 高通量原位结构解析算法主要用于细胞原位等具有叠合蛋白密度样品的目标蛋白结构解析，该算法基于相关性分析，通过施加最优的权重函数，可以在单张冷冻电镜数据上实现目标蛋白质的定位以及高分辨结构解析。由于无需断层重构，原位结构解析的数据采集通量提升了数十倍。

  Categories Structure refinementTool Type: ApplicationTechnologies: C, Python2Download Count: 1608

• 二维冷冻电镜图像去噪软件 冷冻电子显微镜 (cryo-EM) 是一种广泛使用的超微结构测定技术，它通过一组 2D 显微照片构建蛋白质和大分子复合物的 3D 结构。然而，受电子束剂量的限制，冷冻电镜中的显微照片通常具有极低的信噪比 (SNR)，这会影响下游分析的效率和有效性。特别是cryoEM中的噪声不是简单的加性或乘性噪声，其统计特性与自然图像中的噪声有很大不同，极大地束缚了传统去噪方法的性能。在这里，我们提出了 Noise-Transfer2Clean (NT2C)，这是一种用于冷冻电镜的去噪深度神经网络 (DNN)，用于增强图像对比度和恢复标本信号，其主要思想是通过正确学习冷冻电镜图像的噪声分布并将噪声的统计性质转移到降噪器中来提高去噪性能。特别是针对cryo-EM中复杂的噪声模型，我们设计了一种对比度引导的噪声和信号重加权算法，实现了干净噪声的数据合成和数据增强，使我们的方法真正实现了基于噪声真实属性的信号恢复。 我们的工作验证了基于直接从噪声补丁中挖掘复杂的冷冻电镜噪声模式的去噪的可行性。在模拟数据集和真实数据集上的综合实验结果表明，与常用方法相比，NT2C 在图像去噪方面取得了显着的进步，尤其是在背景噪声去除方面。此外，对真实数据集的案例研究表明，NT2C 可以极大地缓解 SNR 对粒子拾取造成的障碍，简化粒子的识别。

  Categories Structure refinementTool Type: ApplicationTechnologies: Python3Download Count: 1588

• 三维重构体图像去噪软件 冷冻电子断层成像技术(Cryo-ET)适用于原位结构解析这一电镜成像领域研究最前沿的方向，是新冠病毒整体解析的主要技术，可进行大分子、病毒体的原位状态直接观测。受限于成像设备以及电子剂量等因素，冷冻电子断层重构体图像通常会表现出低信噪比以及低衬度的特性，从而会影响到下游任务的分析与计算。此外，不同于单颗粒电镜图像，断层图像的数据量通常是有限的，并且断层图像中缺乏明确的ground truth的定义，依赖大数据集的有监督深度学习算法将很难适配到断层图像去噪问题当中。为了解决以上问题，我们提出了一种稀疏约束的自监督冷冻电子断层图像去噪网络Sparsity Constrained Network (SC-Net)。通过结合盲点替换的自监督数据构造与基于一阶导数的稀疏性约束，SC-Net实现了单样本训练数据下的自监督深度去噪模型。在保证训练效率的同时也保证了相对可靠的结构恢复与噪声抑制。与最先进的Noise2Void方案相比，我们的方法有着更为可靠的结构恢复性能，与大数据驱动的Topaz相比，我们的方法在低数据量情形下取得了相近的性能。

  Categories Structure refinementTool Type: ApplicationTechnologies: Python3Download Count: 1975