Topic 13

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893 items. Top items listed below.

BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching 147 43 13 4

Kmer2SNP: reference-free SNP calling from raw reads based on matching 13 4

Network-based imputation of dropouts in single-cell RNA sequencing data 147 43 13 4

scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data 13 4

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements 162 13 4

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities 165 62 13 7 4

scLM: automatic detection of consensus gene clusters across multiple single-cell datasets 147 43 13 4

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data. 13 4

rearrvisr: an R package to detect, classify, and visualize genome rearrangements 13 4

Detection of differential RNA modifications from direct RNA sequencing of human cell lines 147 13 4

Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer 112 13 4

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench 147 13 4

Broccoli: combining phylogenetic and network analyses for orthology assignment 13 4

Rcirc: an R package for circRNA analyses and visualization 13 4

The Gene Expression Deconvolution Interactive Tool (GEDIT): Accurate Cell Type Quantification from Gene Expression Data 13 4

DeepHE: Accurately Predicting Human Essential Genes based on Deep Learning 105 26 13 4

graphsim: An R package for simulating gene expression data from graph structures of biological pathways 13 4

Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model 13 4

AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data 13 4

Coupled Co-clustering-based Unsupervised Transfer Learning for the Integrative Analysis of Single-Cell Genomic Data 147 43 13 4

Liftoff: an accurate gene annotation mapping tool 13 4

miRinGO: Prediction of biological processes indirectly targeted by human microRNAs 13 4

DELPHI: accurate deep ensemble model for protein interaction sites prediction 105 13 4

Deep learning approaches predict non-coding RNA functions from only raw sequence data 162 105 13 4

AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution 147 43 13 4

Balrog: A universal protein model for prokaryotic gene prediction 162 13 4

On the automatic annotation of gene functions using observational data and phylogenetic trees 162 13 4

SubFeat: Feature Subspacing Ensemble Classifier for Function Prediction of DNA, RNA and Protein Sequences 13 4

mbkmeans: fast clustering for single cell data using mini-batch k-means 147 43 13 4

CoCoNet: Boosting RNA contact prediction by convolutional neural networks 105 26 13 4

Real-time resolution of short-read assembly graph using ONT long reads 13 4

Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections 162 13 4

pDriver: A novel method for unravelling personalised coding and miRNA cancer drivers 13 4

S-conLSH: Alignment-free gapped mapping of noisy long reads 13 4

MapCaller - An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data 13 4

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data 147 13 4

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning 162 13 4

DrawAlignR: An interactive tool for across run chromatogram alignment visualization 13 4

Cell-ID: gene signature extraction and cell identity recognition at individual cell level 147 13 4

MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function 13 4

Haplocheck: Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies 13 4

JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation 147 13 4

A Self-Attention Model for Inferring Cooperativity between Regulatory Features 13 4

Deep learning of gene interactions from single cell time-course expression data 147 13 4

A statistical nonparametric method for identifying consistently important features across samples 147 13 4

FEATS: Feature selection based clustering of single-cell RNA-seq data 147 13 4

Bactopia: a flexible pipeline for complete analysis of bacterial genomes 13 4

Choosing representative proteins based on splicing structure similarity improves the accuracy of gene tree reconstruction 162 13 4

Metalign: Efficient alignment-based metagenomic profiling via containment min hash 13 4

Predicting candidate genes from phenotypes, functions, and anatomical site of expression 162 105 13 4

PAN: Personalized Annotation-based Networks for the Prediction of Breast Cancer Relapse 112 13 4

Accurate spliced alignment of long RNAsequencing reads 13 4

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data 13 4

Finding human gene-disease associations using a Network Enhanced Similarity Search (NESS) of multi-species heterogeneous functional genomics data 13 4

XGSEA: CROSS-species Gene Set Enrichment Analysis via domain adaptation 13 4

cognac: rapid generation of concatenated gene alignments for phylogenetic inferencefrom large whole genome sequencing datasets 13 4

ILoReg enables high-resolution cell population identification from single-cell RNA-seq data 147 13 4

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data 13 4

HieRFIT: Hierarchical Random Forest for Information Transfer 147 13 4

Detecting genomic deletions from high-throughput sequence data with unsupervised learning 13 4

New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics 165 13 4

Bayesian non-parametric clustering of single-cell mutation profiles 147 13 4

SCAPP: An algorithm for improved plasmid assembly in metagenomes 162 13 4

LIQA: Long-read Isoform Quantification and Analysis 25 13 4

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification 147 13 4

scGCN: a Graph Convolutional Networks Algorithm for Knowledge Transfer in Single Cell Omics 13 4

Evaluation of consensus strategies for haplotype phasing 145 13 4

Learning a latent representation of human genomics using Avocado 13 4

Dix-seq: An integrated pipeline for fast amplicon data analysis 13 4

KRSA: Network-based Prediction of Differential Kinase Activity from Kinome Array Data 13 4

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data 83 13 4

Partitioning gene-based variance of complex traits by gene score regression 19 13 4

NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data 13 4

MotiMul: A significant discriminative sequence motif discovery algorithm with multiple testing correction 13 4

PickPocket : Pocket binding prediction for specific ligands family using neural networks. 162 105 13 4

pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods 13 4

HASLR: Fast Hybrid Assembly of Long Reads 25 13 4

ECMarker: Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages 105 26 13 4

MACREL: antimicrobial peptide screening in genomes and metagenomes 13 4

A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis 13 4

Automated quality control of next generation sequencing data using machine learning 13 4

MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity 19 13 4

Corna - An Open Source Python Tool For Natural Abundance Correction In Isotope Tracer Experiments 62 13 4

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data 13 4

Varmole: A biologically drop-connect deep neural network model for prioritizing disease risk variants and genes 13 4

STIG: Generation and simulated sequencing of synthetic T cell receptor repertoires 13 4

Alignment of single-cell RNA-seq samples without over-correction using kernel density matching 147 43 13 4

S-IRFindeR: stable and accurate measurement of intron retention 13 4

NanoReviser: An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm 13 4

DEBKS: A Tool to Detect Differentially Expressed Circular RNA 13 4

AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data 13 4

Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices 13 4

Post-prediction inference 13 4

Identification of Conserved Evolutionary Trajectories in Tumors 13 4

Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data from CITE-seq 147 13 4

MetaPrism: A Toolkit for Joint Taxa/Gene Analysis of Metagenomic Sequencing Data 13 4

GRNUlar: Gene Regulatory Network reconstruction using Unrolled algorithm from Single Cell RNA-Sequencing data 13 4

Monet: An open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces 147 13 4

TranSynergy: Mechanism-Driven Interpretable Deep Neural Network for the Synergistic Prediction and Pathway Deconvolution of Drug Combinations 105 13 4

orfipy: a fast and flexible tool for extracting ORFs 13 4