Rahul Agarwal
I'm a Bioinformatician and Programmer
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Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
Rahul Agarwal 4616 days agoiSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 2211 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...Live Webinar on RNA-Seq Data Analysis on 9 Nov 2016
By Strand 3426 days agoLive Webinar on RNA-Seq Data Analysis Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2738 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism
By Rahul Nayak 2204 days agoMCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal...Encode sequencing data freely available to download and use for academic means
By Rahul Agarwal 4376 days ago Comments (3)genome.ucsc.edu - In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed...BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing...
By Jit 2837 days agogithub.com - BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...R package for visualising GO enrichment
By Jit 4611 days agoR package for visualising GO enrichment results as wordclouds is available at CRANBioDBnet
By Jit 3565 days agobiodbnet-abcc.ncifcrf.gov - Database to Database Conversions db2db allows for conversions of identifiers from one database to other database identifiers or annotations. To use db2db select the input type of your data, changing the input type automatically changes the output...WEGO : simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation...
By BioStar 2155 days agowego.genomics.org.cn - WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...
