We ran #deconvolution on the 110 bulk RNA-seq samples, with six selected methods: #DWLS, #bisqueRNA, #MuSiC, #BayesPrism, #hspe, and #CIBERSORTx. The methods returned a wide range of proportion estimates 📊
April 11, 2025 at 2:35 PM
We ran #deconvolution on the 110 bulk RNA-seq samples, with six selected methods: #DWLS, #bisqueRNA, #MuSiC, #BayesPrism, #hspe, and #CIBERSORTx. The methods returned a wide range of proportion estimates 📊
Application of CIBERSORTx and BayesPrism to deconvolution of bulk RNA-seq data from human myocardium and skeletal muscle: Heliyon www.cell.com/heliyon/full...
Application of CIBERSORTx and BayesPrism to deconvolution of bulk RNA-seq data from human myocardium and skeletal muscle
RNA-sequencing (RNA-seq) is an important tool to explore molecular mechanisms of disease.
Technological advances mean this can be performed at the single-cell level, but the
large sample sizes needed ...
www.cell.com
February 16, 2025 at 10:19 PM
Application of CIBERSORTx and BayesPrism to deconvolution of bulk RNA-seq data from human myocardium and skeletal muscle: Heliyon www.cell.com/heliyon/full...
Why does CibersortX no longer like my data….. I would like it to like my data 🤣
Any bioinformatics people on here able to recommend a code dependent immune deconv package that would be great. I’ve got XCell and Quantiseq working in the immundeconv R package but don’t know if they are as respected…
Any bioinformatics people on here able to recommend a code dependent immune deconv package that would be great. I’ve got XCell and Quantiseq working in the immundeconv R package but don’t know if they are as respected…
October 30, 2023 at 8:35 PM
Why does CibersortX no longer like my data….. I would like it to like my data 🤣
Any bioinformatics people on here able to recommend a code dependent immune deconv package that would be great. I’ve got XCell and Quantiseq working in the immundeconv R package but don’t know if they are as respected…
Any bioinformatics people on here able to recommend a code dependent immune deconv package that would be great. I’ve got XCell and Quantiseq working in the immundeconv R package but don’t know if they are as respected…
Anybody around has experience with CibersortX? It has become my new nightmare!
April 4, 2025 at 4:39 PM
Anybody around has experience with CibersortX? It has become my new nightmare!
New CRAN package dicepro with initial version 1.0.2
#rstats
https://cran.r-project.org/package=dicepro
#rstats
https://cran.r-project.org/package=dicepro
CRAN: Package dicepro
Performs semi-supervised deconvolution of bulk RNA sequencing (RNA-seq) data. Known cell-type proportions are estimated using supervised methods – 'CIBERSORTx' (CSx), 'CIBERSORT' (CS), 'FARDEEP' (Fast And Robust DEconvolution of Expression Profiles), and 'DCQ' (Digital Cell Quantifier) – while unknown components are inferred using non-negative matrix factorization ('NMF') with limited-memory Broyden-Fletcher-Goldfarb-Shanno with bounds ('L-BFGS-B') optimization. Hyperparameters are selected automatically using a Pareto-frontier-based approach with knee-point detection, allowing application when the reference signature matrix is incomplete. More details about 'DICEpro' can be found in Ba et al. (2026) <<a href="https://doi.org/10.64898%2F2026.06.17.732876" target="_top">doi:10.64898/2026.06.17.732876</a>>.
cran.r-project.org
June 30, 2026 at 1:02 PM
New CRAN package dicepro with initial version 1.0.2
#rstats
https://cran.r-project.org/package=dicepro
#rstats
https://cran.r-project.org/package=dicepro
New on CRAN: dicepro (1.0.2). View at https://CRAN.R-project.org/package=dicepro
dicepro: Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization
Performs semi-supervised deconvolution of bulk RNA sequencing (RNA-seq) data. Known cell-type proportions are estimated using supervised methods – 'CIBERSORTx' (CSx), 'CIBERSORT' (CS), 'FARDEEP' (Fast And Robust DEconvolution of Expression Profiles), and 'DCQ' (Digital Cell Quantifier) – while unknown components are inferred using non-negative matrix factorization ('NMF') with limited-memory Broyden-Fletcher-Goldfarb-Shanno with bounds ('L-BFGS-B') optimization. Hyperparameters are selected automatically using a Pareto-frontier-based approach with knee-point detection, allowing application when the reference signature matrix is incomplete. More details about 'DICEpro' can be found in Ba et al. (2026) <<a href="https://doi.org/10.64898%2F2026.06.17.732876" target="_top">doi:10.64898/2026.06.17.732876</a>>.
CRAN.R-project.org
June 30, 2026 at 3:25 PM
New on CRAN: dicepro (1.0.2). View at https://CRAN.R-project.org/package=dicepro
Assessing Immune Microenvironment in TCGA-LUAD via CIBERSORTx Using Single-Cell Derived Signature Matrix and ESTIMATE Algorithm https://www.biorxiv.org/content/10.1101/2024.05.08.592760v1
Assessing Immune Microenvironment in TCGA-LUAD via CIBERSORTx Using Single-Cell Derived Signature Matrix and ESTIMATE Algorithm https://www.biorxiv.org/content/10.1101/2024.05.08.592760v1
Lung cancer (LC) remains a significant global health concern, affecting millions worldwide each year
www.biorxiv.org
May 11, 2024 at 1:48 AM
Assessing Immune Microenvironment in TCGA-LUAD via CIBERSORTx Using Single-Cell Derived Signature Matrix and ESTIMATE Algorithm https://www.biorxiv.org/content/10.1101/2024.05.08.592760v1
Unravelling Immune Cell Signatures: CIBERSORTx-assisted Construction of Signature Matrix from Single-Cell Data https://www.biorxiv.org/content/10.1101/2024.05.05.592045v1
Unravelling Immune Cell Signatures: CIBERSORTx-assisted Construction of Signature Matrix from Single-Cell Data https://www.biorxiv.org/content/10.1101/2024.05.05.592045v1
The immune system's intricate orchestration is pivotal in combating infections and diseases, often l
www.biorxiv.org
May 6, 2024 at 5:50 AM
Unravelling Immune Cell Signatures: CIBERSORTx-assisted Construction of Signature Matrix from Single-Cell Data https://www.biorxiv.org/content/10.1101/2024.05.05.592045v1
Went on a tangent and found ecotyper… which of course requires CibersortX… but a new wave of energy has hit to get it working so I can try that out too 🤣
October 30, 2023 at 8:50 PM
Went on a tangent and found ecotyper… which of course requires CibersortX… but a new wave of energy has hit to get it working so I can try that out too 🤣
to ensure the results were not due to differences in cell composition, we used deconvolution (xCell & CIBERSORTx), which indicated a weak to no association with immune cell types. thus, the heterogeneity observed was likely due to regulatory differences in the cancer cells
November 23, 2024 at 1:47 PM
to ensure the results were not due to differences in cell composition, we used deconvolution (xCell & CIBERSORTx), which indicated a weak to no association with immune cell types. thus, the heterogeneity observed was likely due to regulatory differences in the cancer cells
Using #RNAseq in combination with #CIBERSORTx on paired tumor scrapes, 3D organoids and 2D cultured cells, we discovered that zero-passage organoids generally retain the proportion of luminal cells, whereas 2D cultures did not, illustrating the importance of #matrigel cues.
March 28, 2024 at 8:23 PM
Using #RNAseq in combination with #CIBERSORTx on paired tumor scrapes, 3D organoids and 2D cultured cells, we discovered that zero-passage organoids generally retain the proportion of luminal cells, whereas 2D cultures did not, illustrating the importance of #matrigel cues.
Assessing Immune Microenvironment in TCGA-LUAD via CIBERSORTx Using Single-Cell Derived Signature Matrix and ESTIMATE Algorithm https://www.biorxiv.org/content/10.1101/2024.05.08.592760v1
Assessing Immune Microenvironment in TCGA-LUAD via CIBERSORTx Using Single-Cell Derived Signature Matrix and ESTIMATE Algorithm https://www.biorxiv.org/content/10.1101/2024.05.08.592760v1
Lung cancer (LC) remains a significant global health concern, affecting millions worldwide each year
www.biorxiv.org
May 11, 2024 at 1:48 AM
Assessing Immune Microenvironment in TCGA-LUAD via CIBERSORTx Using Single-Cell Derived Signature Matrix and ESTIMATE Algorithm https://www.biorxiv.org/content/10.1101/2024.05.08.592760v1
Unravelling Immune Cell Signatures: CIBERSORTx-assisted Construction of Signature Matrix from Single-Cell Data https://www.biorxiv.org/content/10.1101/2024.05.05.592045v1
Unravelling Immune Cell Signatures: CIBERSORTx-assisted Construction of Signature Matrix from Single-Cell Data https://www.biorxiv.org/content/10.1101/2024.05.05.592045v1
The immune system's intricate orchestration is pivotal in combating infections and diseases, often l
www.biorxiv.org
May 6, 2024 at 5:50 AM
Unravelling Immune Cell Signatures: CIBERSORTx-assisted Construction of Signature Matrix from Single-Cell Data https://www.biorxiv.org/content/10.1101/2024.05.05.592045v1