Robert C. Spitale, Ph.D.
Please note that this page is constantly being updated.
RNA Sequencing Analysis Programs
Note: This list is taken from the RNA-Seq blog, an excellent resource for updated news and information about RNA sequencing data analysis.
ArrayExpressHTS - is an R based pipeline for pre-processing, expression estimation and data quality assessment of high throughput sequencing transcriptional profiling (RNA-seq) datasets.
iAssembler Ð a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs.
Trinity RNA-Seq Assembly Ð software solutions targeted to the reconstruction of full-length transcripts and alternatively spliced isoforms from Illumina RNA-Seq data.
RSEQtools - a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
Myrna - a cloud computing tool for RNA sequence.
MapSplice - Splice Junction Mapping Tool.
Oqtans: Online Quantitative Transcriptome Analysis.
DESeq - Digital gene expresion analysis based on the negative binomial distribution.
MapPER - an RNA-seq paired-end read (PER) protocol.
rQuant.web - is a web service to provide convenient access to tools for the quantitative analysis of RNA-Seq data.
Scripture - is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.
Cufflinks - assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
SpliceMap - SpliceMap is a de novo splice junction discovery tool. It offers high sensitivity and support for arbitrarily long RNA-seq read lengths.
TopHat - is a fast splice junction mapper for RNA-Seq reads.
PALMapper - a combination of the spliced alignment method QPALMA with the short read alignment tool GenomeMapper.
RNA-MATE - A recursive mapping strategy for high-throughput RNA-sequencing data.
ERANGE - Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq
SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome.
Bioconductor - Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
BWA - BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (targe), such as the human reference genome.
CisGenome - An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
GenePattern - is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
Galaxy - Mapping pipeline for Illumina, 454, and SOLiD sequencing data.
MAQ - stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
UCSC Genome Browser - This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.
Crystallography Programs and Resources
Note: This list is taken from the Stanford SLAC website, an excellent resource for obtaining resources focused on crystallography and the analysis of crystallographic data.
Please click on the program name to access the program home page.
| Program | SSRL Manual | Program Manual | Current Version | Last update | Expiration date | License contact/Download site | User Support |
|---|---|---|---|---|---|---|---|
| Data processing and strategy | |||||||
| Mosflm | Mosflm-Scala tutorial | Manual | 7.0.6 | January 2010 | none | Download
from MOSFLM site Download from CCP4 site | yes |
| imosflm | Not available | Manual | 1.0.4 | January 2010 | none | Download | no |
| Scala | Mosflm-Scala tutorial | Manual | 3.3.16 | January 2010 | none | Download from CCP4 site | yes |
| HKL2000 | HKL2000 tutorial | Purchase HKL2000 manual or use
HKL Manual (PDF) | 0.99.700j (pxproc01-16) | Oct 2010 | May 2011 | Iwona Minor | yes |
| XDS/XSCALE | XDS tutorial | Manual | May 10, 2010 | Jan 2011 | May 2011 | Download | yes |
| Web-Ice | Web-Ice Guide | Manual (PDF) | 4.5 | October 2010 | none | Ana Gonzalez | yes |
| Labelit | Not available | Manual | 1.1.7 | April 2010 | none | Download | no |
| BEST | Not available | Manual | 3.1.0c | January 2007 | none | Dowload | no |
| RADDOSE | Not available | Manual | 6.0 | March 2006 | none | Elspeth Garman | no |
| ELVES | Not available | Manual | 1.2.5 | June 2009 | none | Download | no |
| Phasing and Refinement | |||||||
| CCP4 | Not available | Manual | 6.1.13 | June 2010 | none | Download | yes |
| REFMAC | Not available | Manual | 5.5.0110 | June 2010 | none | Download | no |
| PHENIX | Not available | Manual | 1.6.4 (only on pxproc01-16) | August 2010 | none | Download | no |
| Solve/Resolve | Not available | Solve
Manual Resolve Manual | 2.13 | November 2007 | N/A | Download | yes |
| SHELX | Not available | SHELX Manual
(PDF) SHELXC/D/E Manual (PDF) | 2006/3 | January 2007 | None | Download | yes |
| SnB | Not available | Manual | 2.3 | March 2008 | none | Download | no |
| SHARP/autoSHARP | Not available | Manual | 2.2.0 | April 2006 | November 2009 | Download | no |
| ARP/wARP | Not available | Manual | 7.1 | January 2010 | none | Download | no |
| CNS | Not available | Manual | 1.21 | October 2008 | none | Download | no |
| Phaser | Not available | Manual | 2.1.14 | June 2010 | none | Download | no |
| Model Building and Molecular Graphics | |||||||
| Coot | Coot tutorial | Manual (PDF) | 0.6.1 | February 2010 | none | Download | yes |
| O | Not available | Manual | 12.0 | May 2008 | none | Download | no |
| USF | Not available | Manual | N/A | July 2004 | none | USF site | no |
| XtalView | Not available | Manual | N/A | ??? | none | Download | no |
| PyMOL | Not available | Manual | 1.3 | June 2010 | none | Download | no |
| RasMOL | Not available | Manual | 2.7.2.1 | January 2007 /(CCP4 installation) | none | Download
from RasMOL site Download from CCP4 site | no |