R code and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity"

Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses

Gapp, Bianca V
Konopka, Tomasz
Penz, Thomas
Dalal, Vineet
Burckstummer, Tilmann
Bock, Christoph
Nijman, Sebastian MB

May 2016

This dataset contains data files and analysis code associated with manuscript entitled "Parallel rev...

Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer

Martins, Filipe Correia
Couturier, Dominique-Laurent
de Santiago, Ines
Sauer, Carolin Margarethe
Vias, Maria
Angelova, Mihaela
Sanders, Deborah
Piskorz, Anna
Hall, James
Hosking, Karen
Amirthanayagam, Anumithra
Cosulich, Sabina
Carnevalli, Larissa
Davies, Barry
Watkins, Thomas B. K.
Funingana, Ionut G.
Bolton, Helen
Haldar, Krishnayan
Latimer, John
Baldwin, Peter
Crawford, Robin
Eldridge, Matthew
Basu, Bristi
Jimenez-Linan, Mercedes
Mcpherson, Andrew W.
McGranahan, Nicholas
Litchfield, Kevin
Shah, Sohrab P.
McNeish, Iain
Caldas, Carlos
Evan, Gerard
Swanton, Charles
Brenton, James D.

August 2022

The R markdown document MartinsEtAl-Code-Zenodo.Rmd contains the R code used to generate statistical...

FlowSorted.Blood.450k User’s Guide

Andrew E. Jaffe

January 2014

The FlowSorted.Blood.450k package contains publicly available Illumina HumanMethyla-tion450 (“450k”)...

R code and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity"

Falzone Luca

March 2023

R code and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (...

Supplementary Tables and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity"

Falzone Luca

March 2023

Supplementary Tables and raw data of the tentative manuscript entitled "In silico analysis of the So...

Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"

Chen, Yunshun
Pal, Bhupinder
Visvader, Jane E
Smyth, Gordon K

November 2017

This data set provides data files and R code to accompany the article Differential methylation analy...

anilpsori/DNAm_pipelines_and_biomarkers: Analysis code of DNAm data preprocessing and normalization strategies and implementation of DNAm predictors

anilpsori

October 2022

This release contains programming code written in the R language to implement 101 DNAm data preproce...

Computer codes of Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection

Yuchen Jiao

September 2022

"Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular...

MethylCIBERSORT - an R package for methylation based deconvolution of tumour data.

Ankur Chakravarthy PhD

June 2018

Archive contains a readme and an R source package for installation of MethylCIBERSORT. Validation an...

In silico expression profiles of selected genes with altered methylation in breast cancer.

Byungtak Kim (278128)
Seongeun Kang (278129)
Gookjoo Jeong (565911)
Sung-Bin Park (565912)
Sun Jung Kim (278130)

May 2014

<p>Five genes that have shown methylation change in breast cancer were selected, and their expressio...

R code for thermal proteome profiling analysis

Johnson, Fraser
Liu, Alvin
Lockwood, William
Morin, Gregg

June 2022

R code for the analysis of LCS3 thermal proteome profiling in H23 lung cancer adenocarcinoma cells

R code for: Deep immunophenotyping reveals clinically distinct cellular states and ecosystems in large-scale colorectal cancer

Si Li
Tao Pan
Gang Xu
Yueying Gao
Ya Zhang
Qi Xu
Jiwei Pan
Weiwei Zhou
Juan Xu
Qifu Li
Yongsheng Li

June 2023

The codes used to analyze the tumor cellular states and ecosystems in CRC in the manuscript "Deep im...

Additional file 10 of A methylation- and immune-related lncRNA signature to predict ovarian cancer outcome and uncover mechanisms of chemoresistance

Lu Chen (75170)
Wujiang Gao (9412786)
Li Lin (111038)
Chunli Sha (9412780)
Taoqiong Li (9412783)
Qi Chen (144168)
Hong Wei (334335)
Meiling Yang (153319)
Jie Xing (736394)
Mengxue Zhang (2577658)
Shijie Zhao (496441)
Wenlin Xu (53888)
Yuefeng Li (521173)
Lulu Long (7387430)
Xiaolan Zhu (346441)

September 2023

Additional file 10: Figure S2. lncRNAs strongly correlated with methylation genes and immune genes. ...

code

Meritxell Oliva (13840870)

September 2022

Code to generate figures of manuscript 'DNA methylation QTL mapping across diverse human tissues pro...

Gene expression MethylMix: an R package for identifying DNA methylation-driven genes

Olivier Gevaert

August 2016

Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in ca...

Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses

Gapp, Bianca V
Konopka, Tomasz
Penz, Thomas
Dalal, Vineet
Burckstummer, Tilmann
Bock, Christoph
Nijman, Sebastian MB

May 2016

This dataset contains data files and analysis code associated with manuscript entitled "Parallel rev...

Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer

Martins, Filipe Correia
Couturier, Dominique-Laurent
de Santiago, Ines
Sauer, Carolin Margarethe
Vias, Maria
Angelova, Mihaela
Sanders, Deborah
Piskorz, Anna
Hall, James
Hosking, Karen
Amirthanayagam, Anumithra
Cosulich, Sabina
Carnevalli, Larissa
Davies, Barry
Watkins, Thomas B. K.
Funingana, Ionut G.
Bolton, Helen
Haldar, Krishnayan
Latimer, John
Baldwin, Peter
Crawford, Robin
Eldridge, Matthew
Basu, Bristi
Jimenez-Linan, Mercedes
Mcpherson, Andrew W.
McGranahan, Nicholas
Litchfield, Kevin
Shah, Sohrab P.
McNeish, Iain
Caldas, Carlos
Evan, Gerard
Swanton, Charles
Brenton, James D.

August 2022

The R markdown document MartinsEtAl-Code-Zenodo.Rmd contains the R code used to generate statistical...

FlowSorted.Blood.450k User’s Guide

Andrew E. Jaffe

January 2014

The FlowSorted.Blood.450k package contains publicly available Illumina HumanMethyla-tion450 (“450k”)...

R code and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity"

Falzone Luca

March 2023

R code and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (...

Supplementary Tables and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity"

Falzone Luca

March 2023

Supplementary Tables and raw data of the tentative manuscript entitled "In silico analysis of the So...

Data and code for "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"

Chen, Yunshun
Pal, Bhupinder
Visvader, Jane E
Smyth, Gordon K

November 2017

This data set provides data files and R code to accompany the article Differential methylation analy...

anilpsori/DNAm_pipelines_and_biomarkers: Analysis code of DNAm data preprocessing and normalization strategies and implementation of DNAm predictors

anilpsori

October 2022

This release contains programming code written in the R language to implement 101 DNAm data preproce...

Computer codes of Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection

Yuchen Jiao

September 2022

"Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular...

MethylCIBERSORT - an R package for methylation based deconvolution of tumour data.

Ankur Chakravarthy PhD

June 2018

Archive contains a readme and an R source package for installation of MethylCIBERSORT. Validation an...

In silico expression profiles of selected genes with altered methylation in breast cancer.

Byungtak Kim (278128)
Seongeun Kang (278129)
Gookjoo Jeong (565911)
Sung-Bin Park (565912)
Sun Jung Kim (278130)

May 2014

<p>Five genes that have shown methylation change in breast cancer were selected, and their expressio...

R code for thermal proteome profiling analysis

Johnson, Fraser
Liu, Alvin
Lockwood, William
Morin, Gregg

June 2022

R code for the analysis of LCS3 thermal proteome profiling in H23 lung cancer adenocarcinoma cells

R code for: Deep immunophenotyping reveals clinically distinct cellular states and ecosystems in large-scale colorectal cancer

Si Li
Tao Pan
Gang Xu
Yueying Gao
Ya Zhang
Qi Xu
Jiwei Pan
Weiwei Zhou
Juan Xu
Qifu Li
Yongsheng Li

June 2023

The codes used to analyze the tumor cellular states and ecosystems in CRC in the manuscript "Deep im...

Additional file 10 of A methylation- and immune-related lncRNA signature to predict ovarian cancer outcome and uncover mechanisms of chemoresistance

Lu Chen (75170)
Wujiang Gao (9412786)
Li Lin (111038)
Chunli Sha (9412780)
Taoqiong Li (9412783)
Qi Chen (144168)
Hong Wei (334335)
Meiling Yang (153319)
Jie Xing (736394)
Mengxue Zhang (2577658)
Shijie Zhao (496441)
Wenlin Xu (53888)
Yuefeng Li (521173)
Lulu Long (7387430)
Xiaolan Zhu (346441)

September 2023

Additional file 10: Figure S2. lncRNAs strongly correlated with methylation genes and immune genes. ...

code

Meritxell Oliva (13840870)

September 2022

Code to generate figures of manuscript 'DNA methylation QTL mapping across diverse human tissues pro...

Gene expression MethylMix: an R package for identifying DNA methylation-driven genes

Olivier Gevaert

August 2016

Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in ca...

Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses

Gapp, Bianca V
Konopka, Tomasz
Penz, Thomas
Dalal, Vineet
Burckstummer, Tilmann
Bock, Christoph
Nijman, Sebastian MB

May 2016

This dataset contains data files and analysis code associated with manuscript entitled "Parallel rev...

Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer

Martins, Filipe Correia
Couturier, Dominique-Laurent
de Santiago, Ines
Sauer, Carolin Margarethe
Vias, Maria
Angelova, Mihaela
Sanders, Deborah
Piskorz, Anna
Hall, James
Hosking, Karen
Amirthanayagam, Anumithra
Cosulich, Sabina
Carnevalli, Larissa
Davies, Barry
Watkins, Thomas B. K.
Funingana, Ionut G.
Bolton, Helen
Haldar, Krishnayan
Latimer, John
Baldwin, Peter
Crawford, Robin
Eldridge, Matthew
Basu, Bristi
Jimenez-Linan, Mercedes
Mcpherson, Andrew W.
McGranahan, Nicholas
Litchfield, Kevin
Shah, Sohrab P.
McNeish, Iain
Caldas, Carlos
Evan, Gerard
Swanton, Charles
Brenton, James D.

August 2022

The R markdown document MartinsEtAl-Code-Zenodo.Rmd contains the R code used to generate statistical...

FlowSorted.Blood.450k User’s Guide

Andrew E. Jaffe

January 2014

The FlowSorted.Blood.450k package contains publicly available Illumina HumanMethyla-tion450 (“450k”)...

R code and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity"

Abstract

Extracted data

R code and raw data of the tentative manuscript entitled "In silico analysis of the Solute Carrier (SLC) family in cancer indicates a link among DNA methylation, metabolic adaptation, drug response, and immune reactivity"

Abstract

Extracted data

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