In our analysis, we followed the instruction and tutorials provided by the authors of each software package. We used the default parameters of each tool to perform the analysis. The memory limit for all analysis methods is set to 200GB of RAM. ...
17a), all methods were run on a Linux workstation with 40 CPU cores (two Intel Xeon Silver 4210 chips), 250 GB of RAM and NVIDIA GeForce RTX 2080 Ti graphical processing units. Only a single graphical processing unit card was used when training GLUE. Triple-omics integration The scRNA-...
However, there are still batch specific changes, e.g., capture rate of specific genes and differences in sample processing, which affect the single-cell data, beyond dropout. These changes can be wanted (enforced by the experimental setup) or unwanted (stochastic changes in the experimental ...
Ramskold D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol. 2012;30:777–82. https://doi.org/10.1038/nbt.2282. Goetz JJ, Trimarchi JM. Transcriptome sequencing of single ...
All data in this dataset is gathered usingScrapyandCollyframeworks. Starting with version1.0.7crawler has partialrobots.txtsupport and rate limiting. Please open issue if you experience any problems. Don't forget to include your domain. Add this to your robots.txt: ...
Fisher’s exact test was used and the false discovery rate (FDR) was calculated for multiple test correction. Only less than 0.05 (FDR < 0.05) were retained. The complete annotation dataset for biological process, molecular function, and cellular component GO terms was used for analysis. ...
In contrast, the 10x genomics commercial pipeline Cell Ranger costs approximately $20, in large part due to high RAM requirements. Data Quality Analysis of Breast Leukocytes We applied SEQC to each of the 14 inDrop samples and 61 replicates in our data. Each sample had a minimum of 2 ...
(c) program control unit. In addition, two channels of DMA, six on-chip memories, and various externalinterfaces are provided. The on-chip memory consists of two independent memories,each containing a 512×32-bit data RAM, a 512×32-bit data ROM, and a 512×32-bit program RAM. The ...
Data of multiple types, for example, of RNA and protein. Index sorting Fluorescence-activated sorting of cells into known plate locations. In vitro transcription Transcription of a DNA sequence in vitro using the T7 RNA polymerase. CITE-seq and REAP-seq ...
(false discovery rate of less than 0.01; one-cell embryo versus MII-stage oocyte; Fig.5b,c). These genes were significantly enriched for cytoskeleton organization (Fisher’s exact test odds ratio of 4.67;P = 8.5 × 10−9; Supplementary Table4), and includeApcalong with several ...