AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad...2189 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...ust tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-c...e app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large...2189 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...scriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are...2185 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows re...2185 days ago
Epiviz: an interactive visualization tool for functional genomics data.
...pplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd...2179 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...ise ANI computation of large number of genome pairs. More details about its speed, accuracy and potential applications are described here: "High-throughput ANI Analysis of 90K Proka...2174 days ago
REVIGO: Reduced Visualize gene ontology
REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-base...2157 days ago
miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
From list of genes... ... to microRNAs Using established miRNA-interaction databases, miREM combines hypergeometric and expectation-maximization algorithms to sieve through your genetic data for microRNA signatures https://bioinfo-csi.nus.edu.sg/mirem2/2141 days ago
mmgenome: Tools for extracting individual genomes from metagneomes
...t of the process of extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reproducible through the Rmarkdown format. The m...2147 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
...icted to a particular k-mer size and instead uses a two pass method with both a short "k-mer" and a longer "K-mer". This allows FMLRC to correct through low complexity regions that...2147 days ago