Abhimanyu Singh
A bioinformatics beginner
Latest comments
- Jit on Patterns: a modeling tool dedicated to biological network modeling (2058 days ago): https://github.com/fbertran/Patterns
- Abhimanyu Singh on Genome Assembly Tutorial (3008 days ago): This totorial is also very...
- Jit on Next generation sequencing(NGS) books (3869 days ago): Few next generation sequencing resources at...
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Bioinformatics, Genome, NGS, Assembly, Tool, Analysis, Alignment, Genomes, Reads, Read, long, Sequencing, Synteny, Assembler, PacBio, Ancestral, KEGG, Genes, Assemblies, Algorithm, Pipeline, RNA, sequence, annotation, Graph, Books, Lastz, Reference, Mapping, Tutorial, Reconstruction, Format, View, Genomic, Short, Sequences, plot, Gene, Maps, Bacteria, Visual, correction, Variants, Structure, structural, modeling, Method, DISCOVAR, BroadInstitute, SPAdes
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Abhimanyu Singh's bookmarks
odgi: optimized dynamic genome/graph implementation
By Abhimanyu Singh 1138 days agogithub.com - odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently...Apollo: a sequence annotation editor
By Abhimanyu Singh 2028 days agogenomebiology.biomedcentral.com - The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting...The Extensive de novo TE Annotator (EDTA)
By Abhimanyu Singh 2047 days agogithub.com - The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the...Patterns: a modeling tool dedicated to biological network modeling
By Abhimanyu Singh 2060 days ago Comments (1)github.com - It is designed to work with patterned data. Famous examples of problems related to patterned data are: recovering signals in networks after a stimulation (cascade network reverse engineering), analysing periodic signals.jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 2060 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...iRNAD: a computational tool for identifying D modification sites in RNA sequence
By Abhimanyu Singh 2131 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...multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
By Abhimanyu Singh 2131 days agogithub.com - multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de...HumCFS: a database of fragile sites in human chromosomes
By Abhimanyu Singh 2156 days agowebs.iiitd.edu.in - Fragile sites are specific chromosomal region that exhibit an increased frequency of chromosdomal breakge when cells are exposed to replicative stress. Since from the discovery of chromosomal fragile sites/regions (CFS), several line of evidence...GMASS: a novel measure for genomeassembly structural similarity
By Abhimanyu Singh 2163 days agobioinfo.konkuk.ac.kr - The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo...ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
By Abhimanyu Singh 2183 days agogithub.com - ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding...
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