Software
Gene Mapping and Linkage
Linkprep
Creating LINKAGE style .pre and .dat files from AGRF style data. This creates
standard format input files for linkage analysis software from human
genotyping data.
Creating Mapmaker or R/qtl input files
Converts genotyping and phenotyping data into mapmaker style input
files for use with MAPMAKER or R/QTL.
HumanMSD
Creates human genetic maps based on DeCode, Marshfield, and Genethon
genetic maps by using linear interpolation with UCSC physical map.
MouseMSD
A database interface to genetic and physical map data for mouse markers,
catering for aliases (as available on UCSC - January 2007).
Haploclusters
Performs genome linkage disequilibrium (LD) mapping with case and
control haplotype data with both microsatellite and SNP markers.
Linkdatagen
Generates MERLIN and ALLEGRO input files from Affymetrix SNP chips
with marker subsets, using BRLMM genotyping calls, without having to use GCOS.
GBIRP
Genotype-Based Identification of Relative Pairs - identifies pairs of
individuals who may be related to each other by comparing their genotypes.
EffiSim
A script that calculates two measures of the efficiency of a genome-
wide mutation screen for recessive phenotypes and performs simulations
to confirm results
EffiSim Web Interface
This is a web interface to the EffiSim script above.
Quantitative Trait Haplotype Analysis
A program to test whether a quantitative trait loci is in the vicinity
of a number of markers that are fully linked with each other.
Biostatistics
ELDA: Extreme Limiting Dilution Analysis
Fit single-hit model to a dilution
series using complementary log-log binomial regression.
Log Rank Test
The log rank test of Survival Analysis. This is a method of testing
between two survival curves.
Compare Groups of Growth Curves
Compare Groups of Growth Curves performs a permutation test of the difference
between two groups of growth curves. It calculates all pairwise
comparisons between two or more groups of growth curves.
Sequence Analysis
Mapwhere
A program that finds perfect and partial matches to motifs given by
weighted regular expressions
Marcoil
HMM-based coiled-coil prediction program
GABOS/GAFEP
Get A Bit Of Sequence/Get A Few Exon Primers
GAFEP will retrieve primers created by Primer3 around exons and introns selected by GABOS. Large exons/introns will be split to optimum size blocks and small ones will be padded out with adjacent sequence.
Microarrays
LIMMA
An R Library for Linear Models for Microarray Data. Uses linear models
for analysing designed microarray experiments and for assessing
differential expression.
MSigDB Gene Sets
R versions of the MSigDB gene sets.
StatMod
An R Library for Statistical Modelling and biostatistical analysis
including comparison of growth curves and the analysis of randomized
block designs.
illumina
An R Library for preprocessing Illumina Whole Genome Expression BeadChips.
FIRMA
Finding Isoforms with Robust Multichip Analysis.
R code for analysing Affymetrix exon arrays. Estimates gene expression and calculates scores for alternative splicing detection.
Next-Gen Sequencing
GOseq
An R library for performing Gene Ontology (GO) and other category based tests on
RNA-seq data, which corrects for selection bias.
edgeR
An R package (empirical analysis of digital gene expression in R) for differential
expression (DE) analysis of count data e.g. digital gene expression such as RNA-seq or SAGE data.
Other
ParaCountStudio
A program to count cell numbers within an image.