Bioinformatics

EssSubgraph improves performance and generalizability of mammalian essential gene prediction with large networks

1. Haimei Wen
2. Susan Carpenter
3. Karen McGinnis
4. Andrew Nelson
5. Keriayn Smith
6. Tian Hong

Reviewed by GigaScience

GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction

1. Baohua Chen
2. Dongya Wu
3. Guojie Zhang

Reviewed by GigaScience

Improving the Reliability and Quality of Nextflow Pipelines with nf-test

1. Lukas Forer
2. Sebastian Schoenherr

Reviewed by GigaScience

Reproducible processing of TCGA regulatory networks

1. Viola Fanfani
2. Katherine H Shutta
3. Panagiotis Mandros
4. Jonas Fischer
5. Enakshi Saha
6. Soel Micheletti
7. Chen Chen
8. Marouen Ben Guebila
9. Camila M Lopes-Ramos
10. John Quackenbush

Reviewed by GigaScience

The enduring advantages of the SLOW5 file format for raw nanopore sequencing data

1. Hasindu Gamaarachchi
2. Sasha Jenner
3. Hiruna Samarakoon
4. James M. Ferguson
5. Ira W. Deveson

Reviewed by GigaScience

GTestimate: improving relative gene expression estimation in scRNA-seq using the Good–Turing estimator

1. Martin Fahrenberger
2. Christopher Esk
3. Jürgen A Knoblich
4. Arndt von Haeseler

Reviewed by GigaScience

Convolutional neural networks and outline analyses for archaeobotanical studies of domestication and subspecific identification

1. Vincent Bonhomme
2. Laurent Bouby
3. Julien Claude
4. Camille Dham
5. Muriel Gros-Balthazard
6. Sarah Ivorra
7. Angèle Jeanty
8. Clémence Pagnoux
9. Thierry Pastor
10. Jean-Frédéric Terral
11. Allowen Evin

Reviewed by Peer Community in Archaeology

Subtle methodological variations substantially impact correlation test results in ecological time series

1. Caroline Cannistra
2. Linh Hoang
3. Alex E Yuan
4. Wenying Shou

• Curated by eLife

  eLife Assessment

  This study presents a valuable in-depth comparison of statistical methods for the analysis of ecological time series data, and shows that different analyses can generate different conclusions, emphasizing the importance of carefully choosing methods and of reporting methodological details. The evidence supporting the claims, based on simulated data for a two-species ecosystem, is solid, although testing on more complex datasets could be of further benefit. This paper should be of broad interest to researchers in ecology.

Reviewed by eLife