3307 days ago
BBTools for bioinformatician !
...ther lines are generally safe to ignore but they track other things, like read1- or read2-specific data, and random kmers versus the first kmer.It plots a point every X reads (config...2313 days ago
3051 days ago
Ensembl comparative genomics resources
...esentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and di...3031 days ago
R Graphical Cookbook by Winston Chang
...code chunks shown in the text of the book, but in most cases the differences will be that these pages contain additional code to lay out multiple plots on a single "page". The code...2197 days ago
Next generation sequencing in R or bioconductor environment
...tension for genomics data (online manual) Gviz: Plotting data and annotation information along genomic coordinates HilbertVis: Hilbert genome plots GenomeGraphs: Plotting genom...3667 days ago
Apps for Busy Bioinformatics Researchers !!!
...amine the status of genes in common cell lines. A subset of COSMIC containing cell lines can be queried for mutations. Copy Number Variation (CNV) plots from cell lines profiled by G...3584 days ago
R package for visualising GO enrichment
...the GO enrichment results as word clouds and arranges them together with figures of experimental data. This allows us to draw informative summary plots for analyses such as differen...3983 days ago
IPython: Interactive notebooks
The IPython Notebook is a web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. These...3510 days ago
2307 days ago
Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_rea...2289 days ago
Comment on "Sibelia: A comparative genomics tool"
...inimum block size". Blocks located on the positive strand are colored green, while blocks from negative strand are red. By default, "Sibelia" plots only blocks obtained after th...1328 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
Synteny based tool to arrange contigs "r2cat: synteny plots and comparative assembly" http://bibiserv.techfak.uni-bielefeld.de/r2cat https://academic.oup.com/bioinformatics/article/26/4/570/2433691468 days ago