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Results for "Tools"

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  • Rahul Nayak

    Script of scripts: A pragmatic workflow system for daily computational research https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006843 #SoS #Script #Analysis #Tools #Pipeline

    Tags: SoS, Script, Analysis, Tools, Pipeline

    1883 days ago

  • BioJoker

    http://www-labgtp.na.icar.cnr.it/decontaminer/ decontaMiner, a tool for detecting contaminating organisms in human unmapped sequences. #Tools #decontaMiner #Tool #Contamination

    Tags: Tools, decontaMiner, Tool, Contamination

    1824 days ago

  • Rahul Nayak

    gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

    gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. gapFinisher can fill gaps in draft genom...

    Tags: gapFinisher, reliable, gap, filling, pipeline, SSPACE, LongRead, scaffolder, NGS, Tools

    1555 days ago

  • Jit

    Disc usage for a particular user. $ du -sh ~ #Linux #Cluster #Tools

    Tags: Linux, Cluster, Tools

    1538 days ago

  • Abhinav

    Introduction to phylogenies in R

    R phylogenetics is built on the contributed packages for phylogenetics in R, and there are many such packages. Let's begin today by installing a few critical packages, such as ape, phangorn, phytools, and geiger. To get the most recent CRAN version of these packages, you will need to have R 3.3.x...

    Tags: Introduction, phylogenies, R, Tools

    927 days ago

  • Neelam Jha

    Useful Bioinformatics Analysis Tools !

    CoMeta Classificier of reads from metagenomic sequencing experiments. •  Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10(4):1–23, CoMSA Compressor of multiple sequence alignments of proteins. • &...

    Tags: Tools, Bioinformatics, Genome, Programming

    855 days ago

  • Neelam Jha

    Ten quick tips for deep learning in biology https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009803 #Biology #Tools #Learn

    Tags: Biology, Tools, Learn

    760 days ago

  • Shruti Paniwala

    List of comparative genomics resources !

    3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes Compare structural and functional annotations of proteins between sequenced genomes. ARED Organism -- expansion of ARED reveals AU-rich element cluster variations between human...

    Tags: comparative, Genomics, Resources, Tools, Server, Comparative Genomics

    669 days ago

  • Abhinav

    Tools for RNA classification

    barrnap - https://github.com/tseemann/barrnap CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server) CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server) Infernal - ht...

    Tags: RNA, classification, Tools

    536 days ago

  • Abhinav

    Tools for Differential expression analysis

    apeglm - https://bioconductor.org/packages/release/bioc/html/apeglm.html ashr - https://github.com/stephens999/ashr, https://cran.r-project.org/web/packages/ashr/index.html consensusDE - https://bioconductor.org/packages/release/bioc/html/consensusDE.html DES...

    Tags: Differential, expression, analysis, Tools

    536 days ago

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