transcriptomics Archives

Cell Type Prediction with CellKb

Marta Benegas Coll January 23, 2025

Single-cell transcriptomics has revolutionized the way we understand complex biological systems. By enabling researchers to study gene expression at the resolution of individual cells, it uncovers cellular heterogeneity, reveals intricate developmental pathways, and provides insights into disease mechanisms. However, as powerful as single-cell RNA sequencing (scRNA-Seq) is, translating its immense data into meaningful biological insights remains a great challenge. One

Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

Enrique Presa May 22, 2023

Transcriptome reconstruction is a challenging bioinformatic problem. The development of long-read sequencing technologies has made it easier to solve this issue thanks to the possibility of having transcripts entirely contained in a read. In addition, different algorithms have emerged to generate transcriptomes from long-read datasets, such as FLAIR and StringTie2. Both tools can be used for transcriptome reconstruction with long-read data.

Predict coding regions within transcripts in OmicsBox with TransDecoder

Enrique Presa February 4, 2023

Most transcripts assembled from eukaryotic and prokaryotic RNA-Seq data are expected to code for proteins. The most practical procedure to identify likely coding transcripts is a sequence homology search, such as by BLASTX, against sequences from well-annotated and related species. Predicting coding regions is crucial to determine the molecular role that transcripts play in the cell. Unfortunately, such well-annotated nearby

Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

David Seide November 23, 2020

1. Introduction Juvenile rhesus macaques commonly suffer from idiopathic chronic diarrhea (ICD). This disease is characterized by inflammation of the colon and repeated bouts of diarrhea. It is a common cause of morbidity and mortality among macaques because it is unresponsive to drugs. The gut microbiome of macaques with ICD is characterized by abrupt changes when compared to healthy individuals.

Zeroing in on genes involved in courtship song variation in Laupala crickets

Mariana Monteiro June 9, 2020

OmicsBox Supported Project. Researchers: Hayden Waller, Cornell University, USA Background and Project Overview: One of the primary outcomes of speciation – the formation of new species – is the generation of pre-mating barriers that prevent or greatly reduce gene flow. Behavioral changes are perhaps the most potent in the early stages of speciation. In particular, the divergent evolution of sexual

Clustering redundant transcripts in OmicsBox with CD-HIT

Carlos Menor May 8, 2020

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. However, with the advancement of next-generation sequencing technologies, the amount of available sequencing data is growing exponentially. Because of this, assembly algorithms often generate a large number of transcripts. Removing redundancy from such data could be crucial for reducing storage space,

De novo transcriptome analysis in Datura metel

Mariana Monteiro April 29, 2020

De novo transcriptome analysis in Datura metel and identification of genes related to withanolides biosynthesis pathway Researchers: Madhavi Hewadikaram Dr Sanjaya Deepal Bathige Prof. Veranja Karunaratne Project Overview Withanolides are secondary plant compounds that belong to a family of C28 ergostane-type steroidal δ lactones that mainly belong to the family Solanaceae of the plant kingdom. Withanolides have held interest and

Identification and Expression analysis of genes involved in endodormancy break in potato.

Mariana Monteiro March 31, 2020

BioBam Scholarship Supported Project – with OmicsBox. Researchers: Madhuri Gupta Dr. Pushpender Kumar Project and Overview At harvest, potato (Solanum tuberosum L.) tubers, one of the most important crops among vegetables, are dormant and will not sprout. Tubers contain shoot apical meristems on their surface, which can differentiate and grow into a new clone of the parent plant.

Exploring transcriptome completeness in OmicsBox with BUSCO

Carlos Menor February 4, 2020

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. Once the assembly is complete, researchers need to know how good it is or compare the quality of similar assemblies generated by different parameters. There are several ways to characterize the quality of transcriptome assemblies. A good metric of assembly

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Cell Type Prediction with CellKb

Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

Predict coding regions within transcripts in OmicsBox with TransDecoder

Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

Zeroing in on genes involved in courtship song variation in Laupala crickets

Clustering redundant transcripts in OmicsBox with CD-HIT

De novo transcriptome analysis in Datura metel

Identification and Expression analysis of genes involved in endodormancy break in potato.

Exploring transcriptome completeness in OmicsBox with BUSCO

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Differences between Fisher’s Exact Test and GSEA for Functional Enrichment

Reference-free analysis of long-read RNA sequencing for non-model species

OmicsBox in a New Scientific Publication on Sorghum Stress Responses

LongTREC Secondments at BioBam: Advancing Long-Read Transcriptomics Through Collaboration

Cell Type Prediction with CellKb

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