Bioinformatics

ParTIpy: A Scalable Framework for Archetypal Analysis and Pareto Task Inference

1. Philipp S. L. Schäfer
2. Leoni Zimmermann
3. Paul L. Burmedi
4. Avia Walfisch
5. Noa Goldenberg
6. Shira Yonassi
7. Einat Shaer Tamar
8. Miri Adler
9. Jovan Tanevski
10. Ricardo O. Ramirez Flores
11. Julio Saez-Rodriguez

Reviewed by Review Commons

Human single-cell atlas analysis reveals heterogeneous endothelial signaling

1. Zimo Zhu
2. Rongbin Zheng
3. Yang Yu
4. Lili Zhang
5. Kaifu Chen

Reviewed by preLights

Raw signal segmentation for estimating RNA modification from Nanopore direct RNA sequencing data

1. Guangzhao Cheng
2. Aki Vehtari
3. Lu Cheng

• Curated by eLife

  eLife Assessment

  This study presents SegPore, a valuable new method for processing direct RNA nanopore sequencing data, which improves the segmentation of raw signals into individual bases and boosts the accuracy of modified base detection. The evidence presented to benchmark SegPore is solid, and the authors provide a fully documented implementation of the method. SegPore will be of particular interest to researchers studying RNA modifications.

Reviewed by eLife

MorphoNet 2.0: An innovative approach for qualitative assessment and segmentation curation of large-scale 3D time-lapse imaging datasets

1. Benjamin Gallean
2. Tao Laurent
3. Kilian Biasuz
4. Ange Clement
5. Noura Faraj
6. Patrick Lemaire
7. Emmanuel Faure

• Curated by eLife

  eLife Assessment

  This important work presents technical and conceptual advances with the release of MorphoNet 2.0, a versatile and accessible platform for 3D+T segmentation and analysis. The authors provide compelling evidence across diverse datasets, and the clarity of the manuscript together with the software's usability broadens its impact. Although the strength of some improvements is hard to fully gauge given sample complexity, the tool is a significant step forward that will likely impact many biological imaging fields.

Reviewed by eLife

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. Arndt von Haeseler

Reviewed by GigaScience