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• • Jit@jit.aber

  

  Jit bookmarked dupRadar package 2533 days ago

  The dupRadar package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glance

  https://bioconductor.org/packages/3.7/bioc/vignettes/dupRadar/inst/doc/dupRadar.html
• • Jit@jit.aber

  

  Jit asked How to fix the MacOS error for ‘ddalpha’ R package installation ? 2534 days ago

  > install.packages(c('ddalpha', 'recipes'))    There is a binary version available but the source version is later:         binary  source needs_compilation ddalpha  1.3.1 1.3.1.1     ...
• • Jit@jit.aber

  

  Jit bookmarked MUMmer4: A fast and versatile genome alignment system 2534 days ago

  MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...

  https://mummer4.github.io/
• • Rahul Nayak@rahul

  

  Rahul Nayak created a page List of visualization tools for genome alignments 2535 days ago

  Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which...
• • biogeek@biogeek

  

  biogeek posted a new ad in the Opportunity JRF at Jaypee Institute of Information Technology (JIIT), Noida Department of Biotechnology 2535 days ago
• • biogeek@biogeek

  

  biogeek posted a new ad in the Opportunity PostDoc at Jaypee Institute of Information Technology (JIIT), Noida Department of Biotechnology 2535 days ago
• • Jit@jit.aber

  

  Jit bookmarked TelomereHunter 2535 days ago

  TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input...

  http://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked karyoploteR: plot whole genomes with arbitrary data 2535 days ago

  karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...

  https://bernatgel.github.io/karyoploter_tutorial/
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh created a new bio-script Plot the density of genes in R 2535 days ago
• • karimse07@karimse07

  

  karimse07 is now a friend with sahabuddin 2537 days ago

  • karimse07@karimse07

  

  • sahabuddin@sahabuddin

  
• • sahabuddin@sahabuddin

  

  sahabuddin is now a friend with karimse07 2537 days ago

  • sahabuddin@sahabuddin

  

  • karimse07@karimse07

  
• • Jit@jit.aber

  

  Jit commented on a bookmark LASTZ 2538 days ago

  Understanding lastz http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf
• • Archana Malhotra@archana

  

  Archana Malhotra bookmarked zPicture: A dynamic blastz alignment visualization 2538 days ago

  zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding...

  https://zpicture.dcode.org/
• • Archana Malhotra@archana

  

  Archana Malhotra is now a friend with biogeek 2538 days ago

  • Archana Malhotra@archana

  

  • biogeek@biogeek

  
• • biogeek@biogeek

  

  biogeek is now a friend with Archana Malhotra 2538 days ago

  • biogeek@biogeek

  

  • Archana Malhotra@archana

  
• • Neel@neelam

  

  Neel created a page Comprehensive list of visualization tools for biological pathways 2538 days ago

  The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads...
• • Rahul Nayak@rahul

  

  Rahul Nayak answered the question How to extract all the reads mapped at specific region in a genome? 2539 days ago

  samtools index your.bamsamtools view your.bam "chr5:200-6000" > output.bam That would output all reads in chr5 between 200-6000 bp.
• • Poonam Mahapatra@poonam

  

  Poonam Mahapatra asked How to extract all the reads mapped at specific region in a genome? 2539 days ago

   I want to extract all the reads mapped at chr5: 200-6000. 
• • Jit@jit.aber

  

  Jit created a page List of visualization tools for network biology 2539 days ago

  Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis provides the ability to quantify associations between individuals, which...
• • Jit@jit.aber

  

  Jit bookmarked MGcV: the microbial genomic context viewer for comparative genome analysis 2539 days ago

  MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV: Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by selecting the type of identifier...

  http://mgcv.cmbi.ru.nl/

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