Publisher Correction: FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing [0.03%]
出版更正：FIPRESCI：基于液滴微流体组合索引的大量5'端单细胞RNA测序
Yun Li,Zheng Huang,Zhaojun Zhang et al.
Yun Li et al.
Published Erratum
Genome biology. 2023 Apr 21;24(1):88. DOI:10.1186/s13059-023-02944-7 2023
Consequences and opportunities arising due to sparser single-cell RNA-seq datasets [0.03%]
更稀疏的单细胞RNA测序数据集带来的挑战与机遇
Gerard A Bouland,Ahmed Mahfouz,Marcel J T Reinders
Gerard A Bouland
With the number of cells measured in single-cell RNA sequencing (scRNA-seq) datasets increasing exponentially and concurrent increased sparsity due to more zero counts being measured for many genes, we demonstrate here that downstream analy...
satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect [0.03%]
用于变异效应复式测定的模拟和变体调用软件包（SATMUT_UTILS）
Ian Hoskins,Song Sun,Atina Cote et al.
Ian Hoskins et al.
The impact of millions of individual genetic variants on molecular phenotypes in coding sequences remains unknown. Multiplexed assays of variant effect (MAVEs) are scalable methods to annotate relevant variants, but existing software lacks ...
pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls [0.03%]
pycoMeth：一个基于纳米孔甲基化数据的差异甲基化检测工具包
Rene Snajder,Adrien Leger,Oliver Stegle et al.
Rene Snajder et al.
We present pycoMeth, a toolbox to store, manage and analyze DNA methylation calls from long-read sequencing data obtained using the Oxford Nanopore Technologies sequencing platform. Building on a novel, rapid-access, read-level and referenc...
PAUSE: principled feature attribution for unsupervised gene expression analysis [0.03%]
基于原理的特征归因在无监督基因表达分析中的应用
Joseph D Janizek,Anna Spiro,Safiye Celik et al.
Joseph D Janizek et al.
As interest in using unsupervised deep learning models to analyze gene expression data has grown, an increasing number of methods have been developed to make these models more interpretable. These methods can be separated into two groups: p...
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles [0.03%]
_ENCODE直面挑战：对表观基因组图谱跨细胞类型填补方法进行批评式评估
Jacob Schreiber,Carles Boix,Jin Wook Lee et al.
Jacob Schreiber et al.
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what meas...
Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data [0.03%]
利用大规模单细胞数据识别影响基因共表达关系的遗传变异体
Shuang Li,Katharina T Schmid,Dylan H de Vries et al.
Shuang Li et al.
Background: Expression quantitative trait loci (eQTL) studies show how genetic variants affect downstream gene expression. Single-cell data allows reconstruction of personalized co-expression networks and therefore the id...
Meta-Analysis
Genome biology. 2023 Apr 18;24(1):80. DOI:10.1186/s13059-023-02897-x 2023
Metabolic independence drives gut microbial colonization and resilience in health and disease [0.03%]
代谢独立驱动健康和疾病状态下肠道微生物定植及稳定性的建立
Andrea R Watson,Jessika Füssel,Iva Veseli et al.
Andrea R Watson et al.
Background: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the de...
GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species [0.03%]
基于高度寻址字节编码块的并行工具包GBC用于物种极其大规模基因型
Liubin Zhang,Yangyang Yuan,Wenjie Peng et al.
Liubin Zhang et al.
Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly address...
JBrowse 2: a modular genome browser with views of synteny and structural variation [0.03%]
JBrowse 2：一种具有同线型和结构变化视图的模块化基因组浏览器
Colin Diesh,Garrett J Stevens,Peter Xie et al.
Colin Diesh et al.
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplo...