Evaluated articles

Showing page 1 of 19 pages of list content

demuxSNP: supervised demultiplexing scRNAseq using cell hashing and SNPs

This article has 4 authors:
1. Michael P. Lynch
2. Yufei Wang
3. Laurent Gatto
4. Aedin C. Culhane
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Apr 26, 2024Latest activity Dec 5, 2024
stMMR: accurate and robust spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation

This article has 10 authors:
1. Daoliang Zhang
2. Na Yu
3. Wenrui Li
4. Xue Sun
5. Qi Zou
6. Xiangyu Li
7. Zhiping Liu
8. Zhiyuan Yuan
9. Wei Zhang
10. Rui Gao
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Feb 29, 2024Latest activity Dec 5, 2024
De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

This article has 19 authors:
1. Carolina Heloisa de Souza Borges
2. Ricardo Utsunomia
3. Alessandro Varani
4. Marcela Uliano-Silva
5. Lieschen Valeria G. Lira
6. Arno J. Butzge
7. John F. Gomez Agudelo
8. Shisley Manso
9. Milena V. Freitas
10. Raquel B. Ariede
11. Vito A. Mastrochirico-Filho
12. Carolina Penaloza
13. Agustín Barria
14. Fábio Porto-Foresti
15. Fausto Foresti
16. Ricardo Hattori
17. Yann Guiguen
18. Ross D. Houston
19. Diogo Teruo Hashimoto
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Mar 12, 2024Latest activity Dec 5, 2024
CAT Bridge: An Efficient Toolkit for Gene-Metabolite Association Mining from Multi-Omics Data

This article has 11 authors:
1. Bowen Yang
2. Tan Meng
3. Xinrui Wang
4. Jun Li
5. Shuang Zhao
6. Yingheng Wang
7. Shu Yi
8. Yi Zhou
9. Yi Zhang
10. Liang Li
11. Li Guo
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Oct 22, 2024Latest activity Dec 5, 2024
Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

This article has 5 authors:
1. Seth A. Frazer
2. Mahdi Baghbanzadeh
3. Ali Rahnavard
4. Keith A. Crandall
5. Todd H. Oakley
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Feb 14, 2024Latest activity Nov 23, 2024
CoCoPyE: feature engineering for learning and prediction of genome quality indices

This article has 7 authors:
1. Niklas Birth
2. Nicolina Leppich
3. Julia Schirmacher
4. Nina Andreae
5. Rasmus Steinkamp
6. Matthias Blanke
7. Peter Meinicke
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Sep 9, 2024Latest activity Nov 23, 2024
A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)

This article has 7 authors:
1. Abigayle Simpson
2. Elisha M. Wood Charlson
3. Montana Smith
4. Kathleen Beilsmith
5. Ben Koch
6. Ramona L. Walls
7. Roland C. Wilhelm
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jul 17, 2023Latest activity Nov 23, 2024
StereoSiTE: A framework to spatially and quantitatively profile the cellular neighborhood organized iTME

This article has 18 authors:
1. Xing Liu
2. Chi Qu
3. Chuandong Liu
4. Na Zhu
5. Huaqiang Huang
6. Fei Teng
7. Caili Huang
8. Bingying Luo
9. Xuanzhu Liu
10. Min Xie
11. Feng Xi
12. Mei Li
13. Liang Wu
14. Yuxiang Li
15. Ao Chen
16. Xun Xu
17. Sha Liao
18. Jiajun Zhang
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Sep 15, 2023Latest activity Nov 23, 2024
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation

This article has 19 authors:
1. Lara Fuhrmann
2. Kim Philipp Jablonski
3. Ivan Topolsky
4. Aashil A Batavia
5. Nico Borgsmüller
6. Pelin Icer Baykal
7. Matteo Carrara
8. Chaoran Chen
9. Arthur Dondi
10. Monica Dragan
11. David Dreifuss
12. Anika John
13. Benjamin Langer
14. Michal Okoniewski
15. Louis du Plessis
16. Uwe Schmitt
17. Franziska Singer
18. Tanja Stadler
19. Niko Beerenwinkel
Reviewed by GigaScience, GigaByte

This article has 4 evaluationsAppears in 2 listsLatest version Oct 16, 2023Latest activity Nov 10, 2024
TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data

This article has 3 authors:
1. Conor Klamann
2. Christie Lau
3. Gregory W. Schwartz
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Jun 18, 2023Latest activity Sep 3, 2024
MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model

This article has 4 authors:
1. Tao Feng
2. Shufang Wu
3. Hongwei Zhou
4. Zhencheng Fang
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 7, 2023Latest activity Aug 12, 2024
CAT – A Computational Anatomy Toolbox for the Analysis of Structural MRI Data

This article has 6 authors:
1. Christian Gaser
2. Robert Dahnke
3. Paul M Thompson
4. Florian Kurth
5. Eileen Luders
6. Alzheimer’s Disease Neuroimaging Initiative
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Nov 28, 2023Latest activity Aug 12, 2024
Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit

This article has 13 authors:
1. Kari Lavikka
2. Jaana Oikkonen
3. Yilin Li
4. Taru Muranen
5. Giulia Micoli
6. Giovanni Marchi
7. Alexandra Lahtinen
8. Kaisa Huhtinen
9. Rainer Lehtonen
10. Sakari Hietanen
11. Johanna Hynninen
12. Anni Virtanen
13. Sampsa Hautaniemi
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Oct 6, 2023Latest activity Aug 12, 2024
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

This article has 6 authors:
1. Eva Aßmann
2. Shelesh Agrawal
3. Laura Orschler
4. Sindy Böttcher
5. Susanne Lackner
6. Martin Hölzer
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Jun 2, 2023Latest activity Aug 12, 2024
Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging

This article has 9 authors:
1. Laznovsky Jakub
2. Kavkova Michaela
3. Reis Alice
4. Robovska-Havelkova Pavla
5. Krivanek Jan
6. Zikmund Tomas
7. Kaiser Jozef
8. Buchtova Marcela
9. Harnos Jakub
Reviewed by GigaScience

This article has 4 evaluationsAppears in 1 listLatest version Jun 11, 2024Latest activity Jul 31, 2024
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes

This article has 2 authors:
1. Muzaffer Arıkan
2. Thilo Muth
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version Dec 5, 2023Latest activity Jul 31, 2024
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

This article has 6 authors:
1. Nathan J. LeRoy
2. Oleksandr Khoroshevskyi
3. Aaron O’Brien
4. Rafał Stepień
5. Alip Arslan
6. Nathan C. Sheffield
Reviewed by GigaScience

This article has 3 evaluationsAppears in 1 listLatest version May 11, 2024Latest activity Jul 31, 2024
Omada: Robust clustering of transcriptomes through multiple testing

This article has 7 authors:
1. Sokratis Kariotis
2. Tan Pei Fang
3. Haiping Lu
4. Chris Rhodes
5. Martin Wilkins
6. Allan Lawrie
7. Dennis Wang
Reviewed by GigaScience

This article has 6 evaluationsAppears in 1 listLatest version Dec 22, 2022Latest activity Jul 31, 2024
Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

This article has 21 authors:
1. Riccardo Baroncelli
2. José F. Cobo-Díaz
3. Tiziano Benocci
4. Mao Peng
5. Evy Battaglia
6. Sajeet Haridas
7. William Andreopoulos
8. Kurt LaButti
9. Jasmyn Pangilinan
10. Anna Lipzen
11. Maxim Koriabine
12. Diane Bauer
13. Gaetan Le Floch
14. Miia R. Mäkelä
15. Elodie Drula
16. Bernard Henrissat
17. Igor V. Grigoriev
18. Jo Anne Crouch
19. Ronald P. de Vries
20. Serenella A. Sukno
21. Michael R. Thon
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Sep 22, 2022Latest activity Jul 1, 2024
Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

This article has 14 authors:
1. Rafael Moysés Alves
2. Vinicius A. C. de Abreu
3. Rafaely Pantoja Oliveira
4. João Victor dos Anjos Almeida
5. Mauro de Medeiros de Oliveira
6. Saura R. Silva
7. Alexandre R. Paschoal
8. Sintia S. de Almeida
9. Pedro A. F. de Souza
10. Jesus A. Ferro
11. Vitor F. O. Miranda
12. Antonio Figueira
13. Douglas S. Domingues
14. Alessandro M. Varani
Reviewed by GigaScience

This article has 2 evaluationsAppears in 1 listLatest version Dec 23, 2023Latest activity Jul 1, 2024

Evaluated articles

demuxSNP: supervised demultiplexing scRNAseq using cell hashing and SNPs

stMMR: accurate and robust spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

CAT Bridge: An Efficient Toolkit for Gene-Metabolite Association Mining from Multi-Omics Data

Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

CoCoPyE: feature engineering for learning and prediction of genome quality indices

A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)

StereoSiTE: A framework to spatially and quantitatively profile the cellular neighborhood organized iTME

V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation

TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data

MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model

CAT – A Computational Anatomy Toolbox for the Analysis of Structural MRI Data

Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit

Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging

gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

Omada: Robust clustering of transcriptomes through multiple testing

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation