Tag: CIBERSORTx

Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…

Kaiyuan Zhang,1,* Ziyue Luo,1,* Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…

From TPM to raw counts 0 I am deconvoluting a bulk RNASeq experiment using scRNA to generate a signature of cell types using CIBERSORTX. The program asks you bulk data normalized, so I used TPM. The finction ‘high resolution’ returns normalized expressione (I presume) per cell type. To perform differential…

CIBERSORTx error: ‘x’ must be an array of at least two dimensions 0 Hi everyone, I’m new here. I’m using CIBERSORTx to build my own signature matrix for brain related cell type. But every time I run it, it always encountered the following error: Error in base::rowMeans(x, na.rm = na.rm,…

Hello Biostars, I have been stuck on an issue for quite some time now, and I hope someone can help me or point me in the right direction. I’ve received my bulk RNA fastq files and analyzed it in R using DESeq2. I have found an article that provide snRNA-seq…

Technical roadmap Figure 1. Fig. 1 Analysis of endometriosis-related differentially expressed genes Using the limma package, we first normalized the expression profile data of the endometriosis datasets, GSE7305 and GSE11691. The data distribution before and after standardized treatment is revealed in a box plot (Figs. 2A–D). We found that the data after…

Find out if Cibersortx.stanford.edu is working normally or is there a problem today What to do if the site CIBERSORTX.STANFORD.EDU is unavailable? If CIBERSORTX.STANFORD.EDU works, but you cannot access the site or its individual page, try one of the possible solutions: Browser cache. To delete the cache and get the…

Hi, I am trying to run a deconvolution analysis of bulk-RNAseq samples using the LM22 signature matrix provided. I converted all ENSEMBL ID’s to their Symbol, and removed NA and duplicated entries. counts_salmon <- as.data.frame(txi$counts) counts_salmon$symbol <- mapIds(org.Hs.eg.db, keys = rownames(counts_salmon), column = “SYMBOL”, keytype = “ENSEMBL”) counts_salmon <- counts_salmon…

Hi everyone! I have quantified the RNA expression in a large number of samples using kallisto, however, I did not include any bootstrapping in my quantifications since I conducted DE analysis using DESeq2, which can’t make use of that information anyways. I wanted to supplement my DE analysis with cell…

Hello, I am doing deconvolution on bulkRNA data from mice brain. I would like to know the proportions of Oligodendrocytes, astrocyte, etc. According to Cibersortx tutorial 1, my first step is to build a signature matrix file from my own single-cell sequencing data. But I got an error saying ‘object…

Swerdlow, S. H. et al. The 2016 revision of the World Health Organization classification of lymphoid neoplasms. Blood 127, 2375–2390 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Sehn, L. H. & Salles, G. Diffuse large B-cell lymphoma. N. Engl. J. Med. 384, 842–858 (2021). Article  CAS  PubMed  PubMed Central …

Read the Full Video Transcript Charles Ryan: Hello, I’m delighted today to speak with Isra Elhussin, MBDS. Dr Elhussin is actually a PhD candidate at Tuskegee University in Tuskegee, Alabama and will soon be doing a postdoctoral at Johns Hopkins. She was recently named as a next gen star of the…

Tools for bulk RNA-seq celltype deconvolution 2 Hi all, I’ve got some bulk RNA-seq data (mouse brain/hippocampus) and I’m looking for tools to extract celltype composition proportions from the data. I’ve been looking around and most of the tools focus on using associated single-cell data, which I do not have….

CIBERSORTx p-values 1 Hi, I’ve been running CIBERSORTx to analyze some samples. My problem is that for the p-value column all the values I get are 9999. Any thoughts? Thanks. cibersortx • 205 views I figured it out. I should use permuations. Login before adding your answer. Read more here:…

Baseline characteristics We described the baseline clinical and pathological characteristics of TNAC and LK-TNBC in Supplementary Table 1. Only stage at diagnosis was different between TNAC and LK-TNBC (P = 0.03), while no significant differences were observed in other characteristics, including nuclear grade, histologic grade, Ki-67, and status of (neo)adjuvant treatment. Somatic…

In the first segment of our review of epigenetic sequencing methods, we covered methylation detection, chromatin accessibility, and protein-DNA interactions. This final part of our review will break outside of the standard analysis and cover some influential multidimensional methods. Spatial Epigenomics“Epigenetic assays, whether conducted at the single-cell or bulk level,…

CIBERSORTx/fractions docker outputs only zeros if –absolute TRUE 0 Hey everyone, I am using the docker container for CIBERSORTx/fractions. I would like to run it in absolute mode (since from this I can also calculate the relative numbers). This guy also had some trouble using it, but it seems different…

CIBERSORTx hires mode duplicates 0 I recently ran a CIBERSORTx hires run where the output file for one of the cell types (e.g., monocytes) had a few genes with the same expression value across all samples. I was wondering why this was the case and that I should remove them…

Cerejeira, J., Lagarto, L. & Mukaetova-Ladinska, E. B. Behavioral and psychological symptoms of dementia. Front. Neurol. 3, 73 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Murphy, M. P. & LeVine, H. III Alzheimer’s disease and the amyloid-beta peptide. J. Alzheimers Dis. 19, 311–323 (2010). Article  PubMed  PubMed Central  Google…

Creating CIBERSORTx signature matrix 0 Hi all, I want to acknowledge that there are several discussions on Biostars regarding how to build a signature matrix or how to normalize datasets for CIBERSORTx. Nevertheless I would still appreciate some clarification on what I am trying to acheive. I am trying to…

Brain cell type deconvolution 2 Hi all! I am interested in understanding the % of main cell types composing my bulk RNA-seq data from brain (e.g., astrocytes, microglia, neurons, oligodendrocytes). However, from what I gathered, this appears to be an extremely complicated task. I came across CiberSortX, but I couldn’t…

ERROR using CIBERSORTx Docker version 0 Dear Biostars, I have been working with the web version and the docker version of CIBERSORTx. However, I have been getting a very strange result in the docker version, and I don’t know what I am doing wrong. Even using the same data and…

What statistical test to apply for DE after CibersortX deconvolution 0 I am running CibersortX in high-resolution mode (which yields estimates of gene values per sample). After that, I want to perform DE between two conditions on the resulting gene estimates. What statistical test would one need to apply to…

DiMasi, J. A., Grabowski, H. G. & Hansen, R. W. Innovation in the pharmaceutical industry: new estimates of R&D costs. J. Health Econ. 47, 20–33 (2016). Article  PubMed  Google Scholar  Wouters, O. J., McKee, M. & Luyten, J. Estimated research and development investment needed to bring a new medicine to…

Can you extract genes for cluster signatures in CIBERSORTx 1 Hi all, just have a question about running CIBERSORTx. So let’s say that we used LM22 as the signature matrix, is it possible to extract the genes which define a particular cell type’s signature in CIBERSORTx? From another post: “CIBERSORTx…

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

CIBERSORTx Docker version 0 Dear Biostars, I have been working with the web version and the docker version of CIBERSORTx. However, I have been getting a very strange result in the docker version, and I don’t know what I am doing wrong. Even using the same data and parameters as…

Introduction Colorectal cancer (CRC) is a leading cause of cancer-related death1 and its mortality rate is expected to rise worldwide, due to population growth and aging, thus entailing a global public health challenge. CRC mortality is mainly due to therapy resistance and metastasis, which are driven by a small population…

Forum:How does CIBERSORTx deal with multiple HGNC symbol rows 0 After obtaining my counts matrix from salmon and assigning HGNC symbols to my ENGS IDs, I end up with multiple rows with duplicate HGNC symbols due to the nature of converting ENGS to HGNC as expected. However, I’m wondering how…

Gregory et al (2023) used single cell RNA-seq data from three sporadic vestibular schwannoma (VS) from Xu et al (2022) to create VS-specific CIBERSORTx signature matrix and gene expression profile (GEP) files to use for the deconvolution workflow of bulk transcriptomic VS. Deconvolution using these files can be used to…

Introduction Breast cancer is the most prevalent malignancy and the leading cause of cancer death in women worldwide.1 After its diagnosis, the most immediate challenge is to tailor treatment strategies and predict the prognosis; traditional clinicopathologic features, including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2…

Wang, J., Garancher, A., Ramaswamy, V. & Wechsler-Reya, R. J. Medulloblastoma: from molecular subgroups to molecular targeted therapies. Annu. Rev. Neurosci. 41, 207–232 (2018). Article  CAS  PubMed  Google Scholar  Cavalli, F. M. G. et al. Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell 31, 737–754.e736 (2017). Article  CAS  PubMed  PubMed Central …

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

Jianwu1 @stemangiola Finalised benchmark: using new tree (treg as a sibling to t_helper) and the tip nodes for non_hierarchical and cibersortx: PCA as reduction method; Overall hierarchical_pairwise_contrast_bayes_silhouette_penalty gives cell signatures that result in the lowest median deconvolution error, it’s ranked first in dim=4 and dim=10, ranked third in dim=2, and…

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

Integrating Bulk RNA-seq data with Single cell RNA seq data 0 Hello all, recently, I had been trying to integrate bulk RNAseq data into single-cell data where I treat each sample in my bulk RNAseq data as a single cell and integrate it into the single-cell data based on the…