Cell clusters were assigned using the Louvain algorithm at a resolution of 0.8. Cell type identification was performed as above. Analysis of 10x Genomics version 3.1 donor 7 hPBMC data Raw sequencing data in FASTQ format were processed using zUMIs version 2.9.3 with automatic barcode detection ...
To address these challenges, we developed Tempo, a Bayesian algorithm for single-cell phase inference from scRNA-seq data. Through a combination of both simulated and real data analyses, we demonstrate that Tempo yields state-of-the-art point estimates. Moreover, Tempo empowers better phase estim...
we performed Random Forest classification. Random Forest classification49is a supervised ensemble learning algorithm that uses an ensemble of decision trees to partition the feature space such that all of the cells with the same cell type label...
We aim to realistically reconstruct gene expression in scRNA-seq data by using a related hq dataset. Ideally, this expression reconstruction algorithm should meet several requirements [7]. First, it needs to bepreciseand model gene expression values realistically. It shouldn’t remove information of ...
If you use trackpy in published research, please read the sectionCiting Trackpy. Features Basics Thewidely-used particle locating algorithmoriginally implemented by John Crocker and Eric Weeks in IDL is reimplemented in Python. Wherever possible, existing tools from widely-used Python modules are employ...
To eliminate this confounding factor and unmask the underlying microglial heterogeneity, we used an established algorithm to regress out cell cycle effects followed by re-clustering of these P7 microglial cells (Figures S3B and S3C; see STAR Methods). This approach yielded three clusters: P7-C0, ...
Cell Ranger [15] Python/R Cell Ranger constructs a sparse k-nearest neighbors (kNN) graph where cells are linked if they are among the k nearest Euclidean neighbors. The Louvain modularity optimization algorithm is used to find highly connected modules in the graph. Then, hierarchical clustering...
Implement the code to solve the algorithm. General Idea: Create a hashset and count each number. Remove numbers seen a second time. There should be a single number left in hashset. Python Java class Solution: def singleNumber(self, nums: List[int]) -> int: # Create hashset hashset =...
To identify the regulons in GSE131907,SCENICalgorithm was implemented by pySCENIC (v0.10.3) in python (3.6.11) [6]. The filtered single-cell expression matrix was taken as the input, and the co-expression module between TF and potential target genes was constructed and defined as a regulon...
s algorithm to identify barcode multiplets. Following the identification of barcode multiplets in each sample, a new tag (‘DB’) was added to the bam file to represent droplet barcodes. This tag contained either the original corrected barcode from the CB tag (in the case of singlets) or ...