Bioinformatics

Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE

1. Matthew Roberts
2. Julia Ogden
3. AS Mukarram Hossain
4. Anshuman Chaturvedi
5. Alastair RW Kerr
6. Caroline Dive
7. Jennifer Ellen Beane
8. Carlos Lopez-Garcia

• Curated by eLife

  eLife assessment

  The authors have developed a useful and user-friendly software to analyse gene expression data from four datasets representing premalignant lung lesions. This software would be of interest to those working in lung cancer and specifically the pre-malignant space. The major strength is the ease of use while the major limitation is the inability for the user to integrate other datasets.

Reviewed by eLife

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles

1. Varuni Sarwal
2. Jaqueline Brito
3. Serghei Mangul
4. David Koslicki

Reviewed by GigaScience

Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data

1. Tommaso Lanciano
2. Aurora Savino
3. Francesca Porcu
4. Davide Cittaro
5. Francesco Bonchi
6. Paolo Provero

Reviewed by GigaScience

scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

1. Malindrie Dharmaratne
2. Ameya S Kulkarni
3. Atefeh Taherian Fard
4. Jessica C Mar

Reviewed by GigaScience

xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments

1. Jesse Farek
2. Daniel Hughes
3. William Salerno
4. Yiming Zhu
5. Aishwarya Pisupati
6. Adam Mansfield
7. Olga Krasheninina
8. Adam C English
9. Ginger Metcalf
10. Eric Boerwinkle
11. Donna M Muzny
12. Richard Gibbs
13. Ziad Khan
14. Fritz J Sedlazeck

Reviewed by GigaScience

Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation

1. Jorge Avila Cartes
2. Santosh Anand
3. Simone Ciccolella
4. Paola Bonizzoni
5. Gianluca Della Vedova

Reviewed by GigaScience

DeePVP: Identification and classification of phage virion proteins using deep learning

1. Zhencheng Fang
2. Tao Feng
3. Hongwei Zhou
4. Muxuan Chen

Reviewed by GigaScience

Stardust: improving spatial transcriptomics data analysis through space aware modularity optimization based clustering

1. Simone Avesani
2. Eva Viesi
3. Luca Alessandrì
4. Giovanni Motterle
5. Vincenzo Bonnici
6. Marco Beccuti
7. Raffaele Calogero
8. Rosalba Giugno

Reviewed by GigaScience

SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data

1. Yunwei Zhang
2. Germaine Wong
3. Graham Mann
4. Samuel Muller
5. Jean Y H Yang

Reviewed by GigaScience

Meta-Prism 2.0: Enabling algorithm for ultra-fast, accurate and memory-efficient search among millions of microbial community samples

1. Kai Kang
2. Hui Chong
3. Kang Ning

Reviewed by GigaScience