Biostatistics
Biostats materials ... Biostatistics is an innovative field that involves the design, analysis, and interpretation of data for studies in public health and medicine. Biostatistics experts arrive at conclusions about disease and health risks by evaluating and applying mathematical and statistical formulas to the factors that impact health.
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HiCdat
By Jit 3208 days agogithub.com - HiCdat: a fast and easy-to-use Hi-C data analysis tool HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes,...KisSplice
By Jit 3022 days agokissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...WiseScaffolder
By Poonam Mahapatra 3056 days agoabims.sb-roscoff.fr - Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common...CrossMap
By Abhimanyu Singh 3002 days agocrossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10...TEannot
By Jit 3020 days agourgi.versailles.inra.fr - We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the...LUMPY
By Shruti Paniwala 3013 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):...Ka, Ks and Ka/Ks calculations
By Poonam Mahapatra 3009 days agolonglab.uchicago.edu - gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including...Redundans
By Jit 3006 days agogithub.com - Redundans pipeline assists an assembly of heterozygous genomes.Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should...
Assembly tutorial PPT
By Jit 3000 days ago Comments (1)Saved Cornell University assembly workshop PPT. Reference: http://cbsu.tc.cornell.edu/lab/doc/assembly_workshop_20150420_lecture1.pdfOPERA : Optimal Paired-End Read Assembler
By Jit 2998 days agosourceforge.net - OPERA (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end/mate-pair/long reads to order and orient the intermediate contigs/scaffolds assembled in a...
