[PDF] Top 20 Assessment of computational methods for the analysis of single cell ATAC seq data
Has 10000 "Assessment of computational methods for the analysis of single cell ATAC seq data" found on our website. Below are the top 20 most common "Assessment of computational methods for the analysis of single cell ATAC seq data".
Assessment of computational methods for the analysis of single cell ATAC seq data
... to single-cell epigenomic data (including ...clustering analysis, in addition to simple trans- formations like binarizing counts and/or performing a ... See full document
25
Accuracy, robustness and scalability of dimensionality reduction methods for single cell RNA seq analysis
... clustering methods (k-means, hierarchical cluster- ing, and Louvain method) to evaluate the performance of different dimensionality reduction methods for down- stream clustering ...inference methods ... See full document
21
SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... ized cell biology, enabling studies of heterogeneity and transcriptome dynamics of complex tissues at single-cell ...scRNA-seq data is the low capturing and sequencing efficiency af- ... See full document
12
BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
... IMGT data- base [3]; however, it has been estimated that as many as 50% or more of Ig gene segments may be missing ...in Methods) were then used for mapping to identify and retain reads con- taining ... See full document
18
Single-nucleus chromatin accessibility reveals intratumoral epigenetic heterogeneity in IDH1 mutant gliomas
... initial analysis revealed that some cells have exactly the same read sequences; a phenomenon that cannot be explained by Tn5 enzyme-selectivity ...our analysis focused on clean- ing the data and ... See full document
12
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
... accessibility analysis of ATAC-seq data can be sensitive to underlying biases within the data, as might be ...analyzed data set involved disrupting a chromatin remodeler subunit, ... See full document
17
PHLI seq: constructing and visualizing cancer genomic maps in 3D by phenotype based high throughput laser aided isolation and sequencing
... and computational analysis were proposed, each subclone of which is gener- ated through subclonal expansion of progenitor tumor cells that acquired advantageous fitness after undergoing an oncogenic initial ... See full document
17
Identification of transcription factor binding sites using ATAC seq
... HINT- ATAC considers the fifth base of ATAC-seq reads as the cleavage event as in ...the data and is less likely to overfit than k-mer-based approaches, when large sequences need to be ...two ... See full document
21
scPred: accurate supervised method for cell type classification from single cell RNA seq data
... (gamma) cell subtypes: Muraro et ...scRNA-seq data from 1321 cells generated using the Smart-Seq2 protocol, and 1349 cells from Xin et ...“ Methods ” section) using the scores from the aligned ... See full document
17
CIDR: Ultrafast and accurate clustering through imputation for single cell RNA seq data
... scRNA-seq data set [20] as an example to illustrate how to use CIDR to discover limitations in the annota- ...use cell-type markers from an independent study [21] to investigate the cause of these ... See full document
11
Reproducible inference of transcription factor footprints in ATAC seq and DNase seq datasets using protocol specific bias modeling
... site-centric computational footprinting tool where 6-mer DNase bias has been incorporated into the model to esti- mate the bias background in a multinomial mixture frame- work ...of ATAC-seq ... See full document
13
Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
... these computational challenges typically requires the ability to use a programming lan- guage like R [5, 6], limiting accessibility for biologists who only have general computer ...scRNA-Seq data, ... See full document
12
f scLVM: scalable and versatile factor analysis for single cell RNA seq
... a single model, and in particular the modelling of gene set annotations has not previously been considered (see Additional file 1 for full details and a comparison to existing factor ...of ... See full document
13
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA seq data
... to single-exon transcripts, genes with a single transcript isoform that generate just one transcript spe- cies are least accurately quantified by most methods ex- cept Scripture ...that ... See full document
26
Recapitulation-like developmental transitions of chromatin accessibility in vertebrates
... the analysis of ACRs, we prepared two different datasets to ensure that the methods to estimate the evo- lutionary ages did not influence our ...other data- set, all protein-coding genes were ... See full document
15
A short survey of computational analysis methods in analysing ChIP-seq data
... Many computational tools have been designed to find the peaks of the signals corresponding to protein binding ...three computational methods, ChIP-seq processing pipeline (spp), PeakSeq and ... See full document
7
Classification of low quality cells from single cell RNA seq data
... As well as expression patterns that distinguish low from high quality cells, we investigated the relationship be- tween technical features and quality. We found 10 fea- tures that separate the different types of low ... See full document
15
Methods, challenges and potentials of single cell RNA seq
... inner cell mass (ICM) cells to ESCs in mouse embryos ...high cell-to-cell variation for genes expressed at intermediate levels, suggesting that they have a higher propensity for dynamic ... See full document
11
Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks
... enrichment analysis using the Genomic Regions Enrich- ment of Annotation Tool (GREAT) ...general cell functionality terms such as “cell cycle” and “RNA processing” ...the cell cycle and DNA ... See full document
16
Single cell analysis of the inner ear sensory organs
... the cell that includes spatial localization in the tissue, cell surface markers and/ or reporter gene ...of single cells of the inner ear sensory organs, instead of averaged gene expres- sion ... See full document
10
Related subjects