Additional file 1 of stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Wellcome Sanger Institute
Arctic Centre, Univ. of Groningen
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Koen Van den Berge
Charlotte Soneson
Mark D. Robinson
Lieven Clement

August 2017

Abstract RNA sequencing studies with complex designs and transcript-resolution analyses involve mult...

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Van den Berge, Koen
Soneson, Charlotte
Robinson, Mark D
Clement, Lieven

August 2017

RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypo...

Additional file 1: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

Alemu Assefa (5556005)
Katrijn De Paepe (5556008)
Celine Everaert (3994859)
Pieter Mestdagh (105016)
Olivier Thas (639464)
Jo Vandesompele (794)

July 2018

Supplementary figures and methods. Figures and tables that are directly referenced in the main repor...

Additional file 1: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Tianyu Wang (397547)
Boyang Li (4268965)
Craig Nelson (3498350)
Sheida Nabavi (3493139)

January 2019

Supplementary materials (Supplementary Tables S1-S11, Supplementary Figures S1-S31). (DOCX 2225âkb

Additional file 2 of Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Xiaobei Zhou (3576761)
Mark Robinson (210259)

October 2015

Supplementary figures. This file contains the mentioned supplementary figures. (PDF 712 kb

Additional file 1 of TnseqDiff: identification of conditionally essential genes in transposon sequencing studies

Lili Zhao (442802)
Mark Anderson (122462)
Weisheng Wu (4110202)
Harry T. Mobley (4230721)
Michael Bachman (4230718)

July 2017

ROC and False discovery curves for conditional essential gene detection in the first simulation stud...

Additional file 1 of A statistical normalization method and differential expression analysis for RNA-seq data between different species

Yan Zhou (6523)
Jiadi Zhu (5607944)
Tiejun Tong (590731)
Junhui Wang (217439)
Bingqing Lin (556010)
Jun Zhang (48506)

March 2019

The false discovery number at the rates of noise in selected conserved genes being 0, 0.1, 0.2, 0.3,...

Additional file 1: of Connecting genetics and gene expression data for target prioritisation and drug repositioning

Enrico Ferrero (298671)
Pankaj Agarwal (191011)

May 2018

Table S1. List of diseases with a significant overlap between genes differentially expressed and gen...

Additional file 1: of Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

K. Kemper (3511319)
M. Littlejohn (3511313)
T. Lopdell (3511301)
B. Hayes (3511316)
L. Bennett (3511307)
R. Williams (3511298)
X. Xu (771131)
P. Visscher (3511304)
M. Carrick (3511310)
M. Goddard (3486104)

November 2016

Supplementary Materials. This document contains supplementary Tables S1-S5 and supplementary Figures...

Supplemental Material for Deutschman et al., 2018

Emily Deutschman (4512202)
Jacqueline R. Ward (4512196)
Kimberly T. Ho-A-Lim (4977314)
Tyler J. Alban (5493089)
Dongmei Zhang (89650)
Belinda Willard (129588)
Madeleine E. Lemieux (208008)
Justin D. Lathia (81374)
Michelle S. Longworth (173223)

August 2018

File S1 contains supplemental methods and supplemental file legends. Figures S1-S10 are supplemental...

Additional file 4: of DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

Bin Xiong (445687)
Yiben Yang (6595283)
Frank Fineis (6595286)
Ji-Ping Wang (82379)

April 2019

Table S2. This table compares the p values and q values of differential expression analysis by edgeR...

Additional file 8: of The molecular landscape of premenopausal breast cancer

Serena Liao (3582692)
Ryan Hartmaier (109111)
Kandace McGuire (3582695)
Shannon Puhalla (3582689)
Soumya Luthra (732484)
Uma Chandran (732485)
Tianzhou Ma (3582698)
Rohit Bhargava (562035)
Francesmary Modugno (757958)
Nancy Davidson (3512738)
Steve Benz (3582686)
Adrian Lee (3161067)
George Tseng (150934)
Steffi Oesterreich (109122)

August 2015

Stratified gene expression analysis in the Molecular Taxonomy of Breast Cancer International Consort...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Wellcome Sanger Institute
Arctic Centre, Univ. of Groningen
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Koen Van den Berge
Charlotte Soneson
Mark D. Robinson
Lieven Clement

August 2017

Abstract RNA sequencing studies with complex designs and transcript-resolution analyses involve mult...

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Van den Berge, Koen
Soneson, Charlotte
Robinson, Mark D
Clement, Lieven

August 2017

RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypo...

Additional file 1: of Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data

Alemu Assefa (5556005)
Katrijn De Paepe (5556008)
Celine Everaert (3994859)
Pieter Mestdagh (105016)
Olivier Thas (639464)
Jo Vandesompele (794)

July 2018

Supplementary figures and methods. Figures and tables that are directly referenced in the main repor...

Additional file 1: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Tianyu Wang (397547)
Boyang Li (4268965)
Craig Nelson (3498350)
Sheida Nabavi (3493139)

January 2019

Supplementary materials (Supplementary Tables S1-S11, Supplementary Figures S1-S31). (DOCX 2225âkb

Additional file 2 of Do count-based differential expression methods perform poorly when genes are expressed in only one condition?

Xiaobei Zhou (3576761)
Mark Robinson (210259)

October 2015

Supplementary figures. This file contains the mentioned supplementary figures. (PDF 712 kb

Additional file 1 of TnseqDiff: identification of conditionally essential genes in transposon sequencing studies

Lili Zhao (442802)
Mark Anderson (122462)
Weisheng Wu (4110202)
Harry T. Mobley (4230721)
Michael Bachman (4230718)

July 2017

ROC and False discovery curves for conditional essential gene detection in the first simulation stud...

Additional file 1 of A statistical normalization method and differential expression analysis for RNA-seq data between different species

Yan Zhou (6523)
Jiadi Zhu (5607944)
Tiejun Tong (590731)
Junhui Wang (217439)
Bingqing Lin (556010)
Jun Zhang (48506)

March 2019

The false discovery number at the rates of noise in selected conserved genes being 0, 0.1, 0.2, 0.3,...

Additional file 1: of Connecting genetics and gene expression data for target prioritisation and drug repositioning

Enrico Ferrero (298671)
Pankaj Agarwal (191011)

May 2018

Table S1. List of diseases with a significant overlap between genes differentially expressed and gen...

Additional file 1: of Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

K. Kemper (3511319)
M. Littlejohn (3511313)
T. Lopdell (3511301)
B. Hayes (3511316)
L. Bennett (3511307)
R. Williams (3511298)
X. Xu (771131)
P. Visscher (3511304)
M. Carrick (3511310)
M. Goddard (3486104)

November 2016

Supplementary Materials. This document contains supplementary Tables S1-S5 and supplementary Figures...

Supplemental Material for Deutschman et al., 2018

Emily Deutschman (4512202)
Jacqueline R. Ward (4512196)
Kimberly T. Ho-A-Lim (4977314)
Tyler J. Alban (5493089)
Dongmei Zhang (89650)
Belinda Willard (129588)
Madeleine E. Lemieux (208008)
Justin D. Lathia (81374)
Michelle S. Longworth (173223)

August 2018

File S1 contains supplemental methods and supplemental file legends. Figures S1-S10 are supplemental...

Additional file 4: of DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

Bin Xiong (445687)
Yiben Yang (6595283)
Frank Fineis (6595286)
Ji-Ping Wang (82379)

April 2019

Table S2. This table compares the p values and q values of differential expression analysis by edgeR...

Additional file 8: of The molecular landscape of premenopausal breast cancer

Serena Liao (3582692)
Ryan Hartmaier (109111)
Kandace McGuire (3582695)
Shannon Puhalla (3582689)
Soumya Luthra (732484)
Uma Chandran (732485)
Tianzhou Ma (3582698)
Rohit Bhargava (562035)
Francesmary Modugno (757958)
Nancy Davidson (3512738)
Steve Benz (3582686)
Adrian Lee (3161067)
George Tseng (150934)
Steffi Oesterreich (109122)

August 2015

Stratified gene expression analysis in the Molecular Taxonomy of Breast Cancer International Consort...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
Wellcome Sanger Institute
Arctic Centre, Univ. of Groningen
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
University of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Li, Shuang
Schmid, Katharina T.
de Vries, Dylan H.
Korshevniuk, Maryna
Losert, Corinna
Oelen, Roy
van Blokland, Irene V.
Groot, Hilde E.
Swertz, Morris A.
van der Harst, Pim
Westra, Harm-Jan
van der Wijst, Monique G.P.
Heinig, Matthias
Franke, Lude
Faculteit Medische Wetenschappen/UMCG
University of Groningen
Wellcome Sanger Institute
University Medical Center Groningen
Institute of Epidemiology 2
Technical University of Munich
Arctic Centre, Univ. of Groningen
University Medical Center Utrecht
DZHK (German Centre for Cardiovascular Research), Partner site Greifswald

January 2023

Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-1...

Additional file 1 of stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Abstract

Extracted data

Additional file 1 of stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage

Abstract

Extracted data

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