Code

This page keeps track of software/code that we have developed or code from others that we have found useful.


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CAGT is a tool to analyze the heterogeneity and diversity of the magnitude, shape and orientation of patterns of functional genomics signal tracks (such as histone modification ChIP-seq signal) around a specific set of defined genomic anchor points (e.g. TF binding sites or TSSs)  Mar 8, 2014, 4:26 PM Anshul Kundaje
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extractSignal can rapidly extract signal data corresponding to user defined intervals from genome-wide signal tracks (using quick random access). Several input formats are supported for the interval data as well as the signal data. A significant advantage of extractSignal is that it is pretty fast especially when used with mat format genome-wide signal files which allow quick random access. You can also specify meta functions that operate on the signal vectors corresponding to each interval. eg. get the maximum value of signal for each interval. You can also perform specific manipulations of the intervals themselves such as expand or contract the intervals or automatic correction to force all intervals to be equal to the predominant interval length in the dataset.  Mar 8, 2014, 4:26 PM Anshul Kundaje
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The Irreproducible Discovery rate (IDR) pipeline developed for ENCODE and modENCODE for robust automated peak calling.  Mar 8, 2014, 4:26 PM Anshul Kundaje
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Code for paper: Kundaje et al. Combining Sequence and Time Series Expression Data To Learn Transcriptional Modules, 2005  5120k v. 3 Mar 8, 2014, 4:26 PM Anshul Kundaje
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A GALAXY implementation of various tools for the uniform processing ENCODE/modENCODE pipeline  Mar 8, 2014, 4:26 PM Anshul Kundaje
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This package computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data  Mar 8, 2014, 4:26 PM Anshul Kundaje
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Wiggler is the official tool used by the ENCODE consortium to generate uniformly processed genome-wide signal tracks for all ChIP-seq, DNase-seq, FAIRE-seq and MNase-seq datasets. These tracks were used in all the Sept 2012 ENCODE papers (http://nature.com/encode)  Mar 8, 2014, 4:26 PM Anshul Kundaje
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  Mar 8, 2014, 4:27 PM Anshul Kundaje
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  Mar 8, 2014, 4:27 PM Anshul Kundaje
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High-dimensional clustering of large number of points using mixture of gaussians  Mar 8, 2014, 4:27 PM Anshul Kundaje
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Fast clustering of large number of data points based on mixtures of Gaussians  Mar 8, 2014, 4:27 PM Anshul Kundaje
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SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. Dictionary learning and matrix factorization (NMF, sparse PCA, ...) Solving sparse decomposition problems with LARS, coordinate descent, OMP, SOMP, proximal methods Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse group lasso, tree-structured regularization, structured sparsity with overlapping groups,...).  Mar 8, 2014, 4:27 PM Anshul Kundaje
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David Blei's collection of Topic model resources  Mar 8, 2014, 4:27 PM Anshul Kundaje
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