Curator Dashboard

A user friendly software tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Videos uploaded to YouTube by the Brain-Computer Interfaces (BCI) research team, University of Zaragoza.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A web application that allows you to perform a quick and comprehensive methylation analysis of cytosine sites in DNA sequences.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Tool for identification and analysis of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. It may identify the unmethylated and methylated regions for a single sample, the conserved and differential methylation regions with different methylation patterns for paired or multiple samples. It includes four main modules as follows: # Normalization of the sequencing reads of cytosines following guanines; # Identification of the unmethylated (methylated) regions using hotspot extension algorithm; # Identification of conservatively and differentially methylated regionsby combining the combinatorial algorithm for determination of potentially functional regions with the algorithm of analysis of variance (ANOVA) for assess the statistical significance of differentially methylated regions; # Extraction of sequence features and visualization of these potentially functional regions.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A software package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. This QC pipeline supplies a fast, easy-to-use, and parallel processing approach to accomplish the comprehensive QC steps, which could be applied widely to almost all kinds of NGS reads, including genomic, transcriptomic and metagenomic data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Videos uploaded to YouTube by the International Neuroinformatics Coordinating Facility (INCF).

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Videos uploaded to YouTube by the Whole Brain Catalog.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

• Resource
• SciCrunch
• 12 years ago - submitted by Andrea Stagg

The International Neuroinformatics Coordinating Facility (INCF) Neuroinformatics blog.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A database of maize genomic sequences, searchable by BLAST, by repeat sequences, and sequence name, gene name, locus, or other landmark. TIGR is a member of the Consortium for Maize Genomics. The Consortium received a funding award from the National Science Foundation in September 2002, to evaluate two gene-enrichment techniques, methylation filtration and high Cot selection, to sequence the maize 'genespace'. Draft assemblies of 287 maize BAC clones selected by the maize community and the Consortium were also produced in the Consortium project. We have recently developed an improved version of the TIGR annotation pipeline optimized for maize genomic assemblies. The latest maize genomic assemblies obtained by gene-enrichment (AZM5) and the 287 maize draft BAC assemblies have been annotated using the improved pipeline. Gene model annotation and functional annotation can be accessed via the TIGR maize BLAST server or the TIGR maize gbrowse display. The first version of the Maize Repeat Database contained 485 characterized maize repeat sequences from the TIGR Cereal Repeat Database. To these we added repetitive sequences downloaded from GenBank and a file of retrotransposon sequences compiled by Phillip SanMiguel (Purdue University). In addition we searched our maize genomic assemblies (AZMs) to identify new repeats. Any sequence within an AZM that showed at least 80% identity over a minimum stretch of 100 bp with an entry in the TIGR Cereal Repeat Database was coded accordingly and added to the Maize Repeat Database.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A Web-based tool that allows users to input a set of exonic variants to score them for a number of features (such as changes in splicing regulatory elements) that have been shown to be predictive of known genome variations that cause exon skipping or activation of ectopic splice sites. In this way, variants can be either prioritized for further splicing-based functional analysis or the results can be used as further genomic evidence in cases in which the causative variant is already known.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A blog about functional MRI from a lab at UC Berkeley.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A quality control software package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A blog by a neuroscientist (United Kingdom) that takes a skeptical look at his own field, and beyond.

• Resource
• SciCrunch
• 15 years ago - by Anonymous