(pubmed.ncbi.nlm.nih.gov) 那它真的可靠可行吗?现在我们了解下这个TRUST4算法 图1 RNA-seq 数据包含组织或外周血单核细胞 (PBMC) 中表达的 TCR 和 BCR 序列,由于来自 V(D)J 重组和 SHM 的库序列与种系不同,它们通常在读取映射步骤中被消除。所以可用RNA-seq 来重构免疫组库数据。如图1 a, 首先TRUST...
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data (https://pubmed.ncbi.nlm.nih.gov/33986545/) 那它真的可靠可行吗?现在我们了解下这个TRUST4算法 图1 RNA-seq 数据包含组织或外周血单核细胞 (PBMC) 中表达的 TCR 和 BCR 序列,由于来自 V(D)J 重组和 SHM 的库序列与...
The datasets analyzed during the current study are available in public databases such as TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and ICGC(https://dcc.icgc.org/). The source code can be obtained from GitHub (https://github.com/liu-xiaohong/sup...
We used the 4,151F. occidentalisgenome scaffolds (410,700,254 bp) submitted to GenBank by “theFrankliniella occidentaliswhole genome shotgun (WGS) project” (accession JMDY01000000,http://www.ncbi.nlm.nih.gov/Traces/wgs/?val =JMDY01#contigs) for microsatellite discovery. Microsatellites wer...
Single-cell sequence analysis and cell type identification After quality control and removal of the batch effect (Supplementary Fig. 1) between pretreatment (PD-1 antibody combined with chemotherapy, patient 08) and posttreatment (achieving pCR, patient 06) GSE207422 scRNA-seq data, 10,441 single...
Clearly, the maintenance of cellular phenotypes involves coordinated actions with many regulatory factors, including the regulation of internal cellular TFs and external cell-to-cell communication. Thus, we first discovered a sequence of regulons that underpins SPP1+ foamy macrophages using SCENIC anal...
Ultimately, we incorporated six independent cohorts with abundant profiles and complete prognosis information, including TCGA-LUAD (n = 497, https://www.cancer.gov/tcga), GSE72094 (n = 398, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72094) [17], GSE50081 (n =...
(A) tail. Using the sequence information from the 5′ end is also important to distinguish alleles of B-cell receptors and T-cell receptors [69]. In scRNA-seq, both 5′ and 3′ tag protocols have been successfully used, but 3′ tagging is currently the standard. The reason for this ...
Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood
XCVATR performs variant annotation to provide a stable and flexible filter for selecting variants with respect to impact. XCVATR takes the variant annotation file (e.g.,GTF or GFF) and annotates the detected variants with respect to their impact on the protein sequence. These variants are then...