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deepTools
By Martin Jones 4137 days agoUser-friendly tools for the normalization and visualization of deep-sequencing dataLive 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...kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2616 days ago Comments (1)pachterlab.github.io - kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for...RNA-Seq Analysis: A Guide for Bioinformaticians
By LEGE 454 days agoRNA-Seq analysis is a cornerstone of modern transcriptomics, offering bioinformaticians a versatile toolkit for unraveling gene expression and regulation. Mastering RNA-Seq workflows and tools empowers researchers to transform raw sequencing data...GeneSpring webinar- Uncovering mechanisms of hepatotoxicity on 14 June at 8AM PST
By Yeshodari 3210 days agoUncovering Mechanisms of Hepatotoxicity for High Affinity Antisense Oligonucleotides – 3’ end RNA-seq Profiling Using GeneSpring GX High affinity antisense oligonucleotides (ASOs) containing bicylic modifications (BNA) such as locked...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2879 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 2432 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...dna2bit: an ultra-fast and accurate genomic distance estimation software
By LEGE 188 days agogithub.com - dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2711 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...Cleaner BLAST Databases for More Accurate Results
By LEGE 683 days agoRemoving contaminated sequences using NCBI quality assurance tools
