Shruti Paniwala
A Bioinformatician
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Bioinformatics, Genome, NGS, Analysis, Assembly, R, Chromosome, Annotation, alignments, assemblies, Paint, Script, Visualize, Visualization, Contigs, Sequence, Blast, quality, interactive, SV, structural, CNIDARIA, Fast, Reference-free, Phylogenomic, Clustering, Platform, Omics, Anvio, Stats, Assemble, Plot, TGNet, Lumpy, Variation, Structure, ACT, Comparison Tool, Artemis, BBMap, Help, Illumina, PANDASEQ, Alignment, See, View, J-Circos, Biostats, Ingo Ruczinski, book
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Shruti Paniwala's bookmarks
RNAcon: web-server for the prediction and classification of non-coding RNAs
By Shruti Paniwala 2697 days agocrdd.osdd.net - RNAcon is a web-server for the prediction and classification of non-coding RNAs. It uses SVM-based model for the discrimination between coding and ncRNAs and RandomForest-based prediction model for the classification of ncRNAs into different...Assembly Course
By Shruti Paniwala 2704 days agoocw.mit.edu - https://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/lecture-slides/MIT7_91JS14_Lecture6.pdfeQuant : energy-based quality assessment of protein
By Shruti Paniwala 2719 days agobiosciences.hs-mittweida.de - Protein structures are of varying quality. Especially, in-silico modeled structures are prone to contain serious errors, which limit the usefulness and reliability of these particular protein structures.eQuant is a service for structure...J-Circos
By Shruti Paniwala 2847 days agowww.australianprostatecentre.org - Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom...Ideoplot
By Shruti Paniwala 2851 days agogithub.com - Simple ideogram plotting and annotation in R. Basic usage: Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf -or- Rscript Ideoplot.R --annotate annotations.bed Options --ideobed, i A bed file of reference...fineSTRUCTURE v2 & GLOBETROTTER
By Shruti Paniwala 2851 days agopaintmychromosomes.com - Software available at this site FineSTRUCTURE version 2, a pipeline for running ChromoPainter and FineSTRUCTURE for population inference. A GUI is available for interpretation. Download from the Downloads page. FineSTRUCTURE R scripts, a...PANDASEQ
By Shruti Paniwala 2872 days agoneufeldserver.uwaterloo.ca - PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable...BBMap help
By Shruti Paniwala 2977 days agowww.biostarhandbook.com - BBMAP • a solution for everything That content has been reformatted and it is being expanded to include more information. There are common options for most BBMap suite programs and depending on the file extension the input/output format...Artemis Comparison Tool (ACT)
By Shruti Paniwala 3010 days agowww.sanger.ac.uk - ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of...LUMPY
By Shruti Paniwala 3023 days agogithub.com - A probabilistic framework for structural variant discovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6):...
