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+HOMER Program Index
+Below is a quick introduction to the different programs included in HOMER.  Running each program without any arguments will provide basic instructions and a list of command line options.
+FASTA file Motif Discovery
+findMotifs.pl - performs motif analysis with lists of Gene Identifiers or FASTA files (See FASTA file analysis)
+
+homer2 - core component of motif finding (Called by everything else , See FASTA file analysis)
+Gene/Promoter-based Analysis
+findMotifs.pl - performs motif and gene ontology analysis with lists of Gene Identifiers, both promoter and mRNA motifs (See Gene ID Analysis Tutorial)
+
+findGO.pl - performs only gene ontology analysis with lists of Gene Identifiers (Called by findMotifs.pl, See Gene Ontology Analysis)
+loadPromoters.pl - setup custom promoter sets for specialized analysis (See Customization)
+Next-Gen Sequencing/Genomic Position Analysis
+findMotifsGenome.pl - performs motif analysis from genomic positions (See Finding Motifs from Peaks)
+
+makeTagDirectory - creates a "tag directory" from high-throughput sequencing alignment files, performs quality control (See Creating a Tag Directory)
+makeUCSCfile & makeBigWig.pl - create bedGraph file for visualization with the UCSC Genome Browser (See Creating UCSC file)
+findPeaks - find peaks in ChIP-Seq data, regions in histone data, de novo transcripts from GRO-Seq (See Finding ChIP-Seq Peaks)
+analyzeChIP-Seq.pl - automation of programs found above (See Automation of ChIP-Seq analysis)
+
+annotatePeaks.pl - annotation of genomic positions, organization of motif and sequencing data, histograms, heatmaps, and more... (See Annotating Peaks, Quantification)
+analyzeRNA.pl - quantification of RNA levels across transcripts (See RNA quantification)
+analyzeRepeats.pl - quantification of RNA levels across repeats (See RNA quantification)
+getDiffExpression.pl - Calculate differential enrichment of RNA-seq/ChIP-seq/ATAC-seq data (See RNA quantification)
+getDifferentialPeaks - find differentially bound regions from ChIP/ATAC-seq experiments
+getDifferentialPeaksReplicates.pl - perform peak finding/Differential peak detection taking into account replicates
+
+mergePeaks - find overlapping peak positions (See Comparing ChIP-Seq Peaks)
+
+homerTools - basic sequence manipulation (See Sequence Manipulation)
+tagDir2bed.pl - output tag directory as an alignment BED file (See Miscellaneous)
+bed2pos.pl, pos2bed.pl - convert between HOMER peak file format and BED file format (See Miscellaneous)
+
+checkPeakFile.pl - use this to see if your peak file is in the correct format
+removeOutOfBoundsReads.pl - remove reads found outside acceptable chromosome limits
+
+annotateTranscripts.pl - annotation of de novo identified transcripts
+
+Motif Manipulation
+compareMotifs.pl - checks a library of motifs for known motifs, creates in HTML output summarizing motif results (described here).
+motif2Logo.pl - creates a PNG or PDF logo from any motif file.
+revoppMotif.pl - creates a new motif file reflecting the nucleotide preferences of the opposite strand.
+seq2profile.pl - creates a new motif file from a consensus sequence
+
+Hi-C Analysis Programs
+analyzeHiC - primary analysis program - generates interaction matrices, normalization, identification of significant interactions, clustering of domains, generates Circos plots (most of the following programs use this one internally, See Hi-C analysis)
+
+runHiCpca.pl - automated PCA analysis on Hi-C data to identify "compartments" (see Hi-C PCA analysis)
+getHiCcorrDiff.pl - calculates the difference in correlation profiles between two Hi-C experiments (see Hi-C PCA analysis)
+findHiCCompartments.pl - find continuous or differential regions from PCA/corrDiff results that describe what compartment regions of DNA belong to (see Hi-C PCA analysis)
+
+findHiCInteractionsByChr.pl - helps automate the finding of high-resolution intra-chromosomal interactions (see Finding Hi-C Interactions)
+annotateInteractions.pl - program for re-analysis of significant interactions, such as relating them to ChIP-Seq peaks (see Annotating Interactions)
+
+SIMA.pl - Novel tool to boost sensitivity by pooling features together when performing interaction calculations. (see SIMA analysis)
+
+Additional Utilities that may be useful (and sub-programs used by those above)
+
+addData.pl, addDataHeader.pl, mergeData.pl - tools for joining/merging tab separated flat files
+
+homerTools extract - extract genomic sequence for peaks from a peak file.
+homerTools freq - finds nucleotide/dinucleotide frequencies of a collection of sequence and GC/CpG content.
+getPeakTags - finds sequencing tags associated with genomic positions.
+scanMotifGenomeWide.pl - look for all instances of a motif in the genome.
+
+
+tagDir2bed.pl - convert *.tags.tsv file directory into a BED file for use with other programs
+
+homer2 - new motif finding program
+homer - original motif finding program (not used anymore)
+
+getTopPeaks.pl - return peaks with the best peak scores.
+getFocalPeaks.pl - return peaks with the highest focus ratios.
+assignGenomeAnnotation - assign peaks to specific annotations in the genome
+
+fasta2tab.pl, tab2fasta.pl - convert between HOMER-style sequence file and a FASTA file.
+
+changeNewLine.pl - converts mac and dos formated text files (new lines of "\r" and "\r\n") to UNIX style ("\n").