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http://tmaj.pathology.jhmi.edu/
Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
Proper citation: TMAJ (RRID:SCR_005601) Copy
http://bowtie-bio.sourceforge.net/myrna/index.shtml
A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.
Proper citation: Myrna (RRID:SCR_006951) Copy
http://bowtie-bio.sourceforge.net/index.shtml
Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
Proper citation: Bowtie (RRID:SCR_005476) Copy
http://ccb.jhu.edu/software/sim4cc/
Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.
Proper citation: sim4cc (RRID:SCR_001204) Copy
http://ccb.jhu.edu/software/hisat2/index.shtml
Graph-based alignment of next generation sequencing reads to a population of genomes.
Proper citation: HISAT2 (RRID:SCR_015530) Copy
Ratings or validation data are available for this resource
http://ccb.jhu.edu/software/tophat/index.shtml
Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
Proper citation: TopHat (RRID:SCR_013035) Copy
http://ls-snp.icm.jhu.edu/ls-snp-pdb/
A web tool for genome-wide annotation of human SNPs.
Proper citation: LS-SNP/PDB (RRID:SCR_010774) Copy
http://ccb.jhu.edu/software/FLASH/
Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.
Proper citation: FLASH (RRID:SCR_005531) Copy
http://ccb.jhu.edu/software/glimmer/index.shtml
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Proper citation: Glimmer (RRID:SCR_011931) Copy
Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.
Proper citation: PyRosetta (RRID:SCR_018541) Copy
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