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

Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah Dueck (3461837)
Rizi Ai (2343607)
Adrian Camarena (3461816)
Bo Ding (210928)
Reymundo Dominguez (3461819)
Oleg Evgrafov (392965)
Jian-Bing Fan (28237)
Stephen Fisher (3461825)
Jennifer Herstein (3461804)
Tae Kim (3405566)
Jae Kim (2100565)
Ming-Yi Lin (237662)
Rui Liu (54031)
William Mack (3461807)
Sean McGroty (3461831)
Joseph Nguyen (3461810)
Neeraj Salathia (18709)
Jamie Shallcross (3461834)
Tade Souaiaia (3291015)
Jennifer Spaethling (3461813)
Christopher Walker (200465)
Jinhui Wang (37220)
Kai Wang (21246)
Wei Wang (17594)
Andre Wildberg (3461828)
Lina Zheng (331151)
Robert Chow (3443600)
James Eberwine (253973)
James Knowles (3461822)
Kun Zhang (108291)
Junhyong Kim (6423)

November 2016

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental ...

Additional file 1: of Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

Luis Nagai (6492632)
Sung-Joon Park (548075)
Kenta Nakai (408)

March 2019

This file includes: detailed information from data used, including statistical information of reads ...

Additional file 1: of The impact of pharmacokinetic gene profiles across human cancers

Michael Zimmermann (203279)
Terry Therneau (5245403)
Jean-Pierre Kocher (179225)

May 2018

PK gene profiles across human cancers. This file contains additional text and figures that support t...

Additional file 2: 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

Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list...

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 3: 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

Significant GO terms with their negative log transform of their q-values for each tool. (CSV 24âkb

Additional file 1: of UMI-count modeling and differential expression analysis for single-cell RNA sequencing

Wenan Chen (5127059)
Yan Li (23143)
John Easton (4615627)
David Finkelstein (222792)
Gang Wu (23885)
Xiang Chen (10398)

May 2018

This file includes: (1) supplementary methods describing details in single cell quality control and ...

Additional file 3: 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 data. Detailed results of concordance analysis of DE tools. (HTML 15901 kb

Additional file 2: 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 data. Detailed results of comparisons of normalization methods. (HTML 2067 kb

Additional file 5: of Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

Claire Williams (2513419)
Alyssa Baccarella (3095256)
Jay Parrish (1834015)
Charles Kim (2529652)

January 2017

Table of number of significant genes identified, for each workflow against each reference dataset. (...

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 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 5: 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 data (A and B). Results of simulation quality assessment. (ZIP 8405 kb

Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah Dueck (3461837)
Rizi Ai (2343607)
Adrian Camarena (3461816)
Bo Ding (210928)
Reymundo Dominguez (3461819)
Oleg Evgrafov (392965)
Jian-Bing Fan (28237)
Stephen Fisher (3461825)
Jennifer Herstein (3461804)
Tae Kim (3405566)
Jae Kim (2100565)
Ming-Yi Lin (237662)
Rui Liu (54031)
William Mack (3461807)
Sean McGroty (3461831)
Joseph Nguyen (3461810)
Neeraj Salathia (18709)
Jamie Shallcross (3461834)
Tade Souaiaia (3291015)
Jennifer Spaethling (3461813)
Christopher Walker (200465)
Jinhui Wang (37220)
Kai Wang (21246)
Wei Wang (17594)
Andre Wildberg (3461828)
Lina Zheng (331151)
Robert Chow (3443600)
James Eberwine (253973)
James Knowles (3461822)
Kun Zhang (108291)
Junhyong Kim (6423)

November 2016

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental ...

Additional file 1: of Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

Luis Nagai (6492632)
Sung-Joon Park (548075)
Kenta Nakai (408)

March 2019

This file includes: detailed information from data used, including statistical information of reads ...

Additional file 1: of The impact of pharmacokinetic gene profiles across human cancers

Michael Zimmermann (203279)
Terry Therneau (5245403)
Jean-Pierre Kocher (179225)

May 2018

PK gene profiles across human cancers. This file contains additional text and figures that support t...

Additional file 2: 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

Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list...

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 3: 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

Significant GO terms with their negative log transform of their q-values for each tool. (CSV 24âkb

Additional file 1: of UMI-count modeling and differential expression analysis for single-cell RNA sequencing

Wenan Chen (5127059)
Yan Li (23143)
John Easton (4615627)
David Finkelstein (222792)
Gang Wu (23885)
Xiang Chen (10398)

May 2018

This file includes: (1) supplementary methods describing details in single cell quality control and ...

Additional file 3: 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 data. Detailed results of concordance analysis of DE tools. (HTML 15901 kb

Additional file 2: 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 data. Detailed results of comparisons of normalization methods. (HTML 2067 kb

Additional file 5: of Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

Claire Williams (2513419)
Alyssa Baccarella (3095256)
Jay Parrish (1834015)
Charles Kim (2529652)

January 2017

Table of number of significant genes identified, for each workflow against each reference dataset. (...

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 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 5: 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 data (A and B). Results of simulation quality assessment. (ZIP 8405 kb

Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah Dueck (3461837)
Rizi Ai (2343607)
Adrian Camarena (3461816)
Bo Ding (210928)
Reymundo Dominguez (3461819)
Oleg Evgrafov (392965)
Jian-Bing Fan (28237)
Stephen Fisher (3461825)
Jennifer Herstein (3461804)
Tae Kim (3405566)
Jae Kim (2100565)
Ming-Yi Lin (237662)
Rui Liu (54031)
William Mack (3461807)
Sean McGroty (3461831)
Joseph Nguyen (3461810)
Neeraj Salathia (18709)
Jamie Shallcross (3461834)
Tade Souaiaia (3291015)
Jennifer Spaethling (3461813)
Christopher Walker (200465)
Jinhui Wang (37220)
Kai Wang (21246)
Wei Wang (17594)
Andre Wildberg (3461828)
Lina Zheng (331151)
Robert Chow (3443600)
James Eberwine (253973)
James Knowles (3461822)
Kun Zhang (108291)
Junhyong Kim (6423)

November 2016

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental ...

Additional file 1: of Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

Luis Nagai (6492632)
Sung-Joon Park (548075)
Kenta Nakai (408)

March 2019

This file includes: detailed information from data used, including statistical information of reads ...

Additional file 1: of The impact of pharmacokinetic gene profiles across human cancers

Michael Zimmermann (203279)
Terry Therneau (5245403)
Jean-Pierre Kocher (179225)

May 2018

PK gene profiles across human cancers. This file contains additional text and figures that support t...

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

Abstract

Extracted data

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

Abstract

Extracted data

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