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-based...2113 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entir...2047 days ago
2040 days ago
EyeChrom: Visualizing Chromosome Count Data From Plants
It's goal is to show chromosmal data per genus. Select the genus, and the plot will show the records found for it in the Chromosome Counts Database. note: Report an issue via Gihub:...1951 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more div...0-start from begining(storing kmers in bloom filter) ; 1-start from count kmers showed up in bloom filt...1559 days ago
1423 days ago
k-mers tutorial - classification and taxonomy
...along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently. More recen...990 days ago
RNA-seq workflow: gene-level exploratory analysis and differential expression
...ing Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analy...946 days ago
Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair...808 days ago
SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
...gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistic...804 days ago