<i>RNAlysis</i>: analyze your RNA sequencing data without writing a single line of code

Teichman, Guy; Cohen, Dror; Ganon, Or; Dunsky, Netta; Shani, Shachar; Gingold, Hila; Rechavi, Oded

doi:10.1101/2022.11.25.517851

Cited by 4 publications

(4 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some progress is being made to make web-based point-and-click tools more reproducible. The Galaxy, GenePattern and RNAlysis projects offer graphical tools to create, edit and import workflows that enable reproducibility [71][72][73]. The Degust differential expression suite is a graphical interface to popular expression tools like edgeR and limma and allows users to download the computer script to facilitate future non-interactive reproducibility [74].…”

Section: Discussionmentioning

confidence: 99%

A recipe for extremely reproducible enrichment analysis (and why we need it)

Bora,

Ziemann

2023

Preprint

View full text Add to dashboard Cite

Unreliable and irreproducible research is a significant problem that wastes resources and risks undermining the public perception of science. Previous work has highlighted that published enrichment analyses frequently suffer from statistical and reporting flaws. We sought to determine whether this translates into irreproducibility by examining whether the findings of 20 open-access articles published in 2019 describing enrichment analysis with the popular DAVID suite were reproducible. We find that only four articles exhibited a high degree of concordance, while seven exhibited major discrepancies, which we mainly ascribe to deficiencies in methodological reporting. As the tool version used is no longer available, all articles using this tool pre-2021 (~20,800 studies) including this sample of 20 articles are no longer able to be reproduced with the original tools. Based on this, we suggest that results from web-based tools without long-term preservation features should not be included in scientific publications due to the threat of link decay and short reproducibility horizon. Relying exclusively on webtools for analysis may also be in breach of institutional and funder data preservation mandates. We advocate for the adoption of extremely reproducible research workflows, and we provide a detailed protocol for how to achieve it for enrichment analysis using a combination of best practices including literate programming, version control, containerisation, documentation and persistent sharing of data and software.

show abstract

Section: Discussionmentioning

confidence: 99%

A recipe for extremely reproducible enrichment analysis (and why we need it)

Bora,

Ziemann

2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Genes were regarded as differentially expressed if they passed the criterion ofFDR <= 0.1. Further analysis was performed using the python-based package RNAlysis (Teichman et al 2023, Python package version 2.1.1).…”

Section: Methodsmentioning

confidence: 99%

A Tunable and Druggable Mechanism to Delay Forgetting of Olfactory Memories inC. elegans

Berliner,

Goldstein,

Teichman

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

The poet W.B Yeats wrote that "All that is personal soon rots, it must be packed in ice or salt". Here we show that in Caenorhabditis elegans nematodes, simple animals with just 302 neurons, memories are preserved on ice and in lithium salt. C. elegans nematodes can form associative memories, which are typically forgotten quickly. We discovered that when placed on ice, worms delay forgetting of specific olfactory memories by at least 8-fold. Delayed forgetting was canceled completely when the worms were gradually adapted to low temperatures, owing to a genetically-encoded program that turns acclimated worms cold-tolerant. RNA-seq, mutant analyses, and pharmacological assays revealed that regulation of membrane properties switches cold-induced delayed forgetting ON and OFF, and, remarkably, that lithium delays forgetting only in cold-sensitive but not cold-tolerant worms. We found that downregulation of the diacylglycerol pathway in the AWC sensory neurons is essential for lithium-mediated delayed forgetting, and using neuronal activity recordings located the memory trace to the downstream AIY interneurons. We suggest that the awesome genetic tractability of C. elegans might be harnessed to study the effects of lithium and cold temperatures on the brain, why it influences psychiatric disorders, and even more fundamentally how memory is stored and lost.

show abstract

“…The cluster maps reinforce the presence of DEGs unique to each sample, and the potential effects of treatment on the DEGs. Gene set enrichment analysis for the mouse and human mapped genes was performed, using the KEGG7 database 50 (www.kegg.jp) and RNAlysis software 51 to identify the biological pathways that are significantly associated with each sample, and to assess the influence of treatment. We considered KEGG terms with p-adj < 0.05 as significant enrichment.…”

Section: Rna-seq Analysesmentioning

confidence: 99%

Peristromal niches protect lung cancers from targeted therapies through a combined effect of multiple molecular mediators

Desai,

Miti,

Prabhakaran

et al. 2024

Preprint

View full text Add to dashboard Cite

Targeted therapies directed against oncogenic signaling addictions, such as inhibitors of ALK in ALK+ NSCLC often induce strong and durable clinical responses. However, they are not curative in metastatic cancers, as some tumor cells persist through therapy, eventually developing resistance. Therapy sensitivity can reflect not only cell-intrinsic mechanisms but also inputs from stromal microenvironment. Yet, the contribution of tumor stroma to therapeutic responses in vivo remains poorly defined. To address this gap of knowledge, we assessed the contribution of stroma-mediated resistance to therapeutic responses to the frontline ALK inhibitor alectinib in xenograft models of ALK+ NSCLC. We found that stroma-proximal tumor cells are partially protected against cytostatic effects of alectinib. This effect is observed not only in remission, but also during relapse, indicating the strong contribution of stroma-mediated resistance to both persistence and resistance. This therapy-protective effect of the stromal niche reflects a combined action of multiple mechanisms, including growth factors and extracellular matrix components. Consequently, despite improving alectinib responses, suppression of any individual resistance mechanism was insufficient to fully overcome the protective effect of stroma. Focusing on shared collateral sensitivity of persisters offered a superior therapeutic benefit, especially when using an antibody-drug conjugate with bystander effect to limit therapeutic escape. These findings indicate that stroma-mediated resistance might be the major contributor to both residual and progressing disease and highlight the limitation of focusing on suppressing a single resistance mechanism at a time.

show abstract

RNAlysis: analyze your RNA sequencing data without writing a single line of code

Cited by 4 publications

References 48 publications

A recipe for extremely reproducible enrichment analysis (and why we need it)

A recipe for extremely reproducible enrichment analysis (and why we need it)

A Tunable and Druggable Mechanism to Delay Forgetting of Olfactory Memories inC. elegans

Peristromal niches protect lung cancers from targeted therapies through a combined effect of multiple molecular mediators

Contact Info

Product

Resources

About