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NanoPack: visualizing and processing long-read sequencing data
By Jit 2454 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2304 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...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1919 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtJuicebox: Visualization and analysis software for Hi-C data
By Jit 1895 days agogithub.com - Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is...Useful links to therapy, disease, drug and drug-target network data:
By Jit 1793 days agoUseful resources to therapy, disease, drug and drug-target network dataMAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1615 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1160 days agogithub.com - 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 coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Powerful books for learning data analysis with R
By LEGE 337 days agohttps://r-graphics.org/ - R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 225 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...
A guide for complete R beginners :- Getting data into R
Last updated 3717 days ago by Archana MalhotraFor a beginner this can be is the hardest part, it is also the most important to get right. It is possible to create a vector by typing data directly into R using the combine function ‘c’ x same as x creates the vector x...
