Abhimanyu Singh
A bioinformatics beginner
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LSC :a long read error correction tool
By Jit 2335 days agowww.healthcare.uiowa.edu - Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2315 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...ClipCrop: a tool for detecting structural variations with single-base resolution using...
By Rahul Nayak 2272 days agogithub.com - This is a tool for detecting structural variations using soft-clipping information From SAM files. https://github.com/shinout/clipcropiRNAD: a computational tool for identifying D modification sites in RNA sequence
By Abhimanyu Singh 2048 days agolin-group.cn - iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the...AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome...
By Jit 1827 days agogithub.com - We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1772 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
By Jit 1680 days agogithub.com - Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 1585 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1488 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...Comparative genomics visualisation tools !
By Neel 1040 days agocmdcolin.github.io - Comparative genomics visualisation tools !
