Here is a list of the packages that are distributed with Macaulay2. The ones that have been refereed are marked with a star.
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AbstractToricVarieties -- links abstract simplicial (normal) toric varieties to Schubert2
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AdjointIdeal -- adjoint ideals of plane curves and related computations
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AlgebraicSplines -- splines on simplicial complexes, polytopal complexes, and graphs
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AnalyzeSheafOnP1 -- decompose a Sheaf on P1
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BeginningMacaulay2 -- Mathematicians' Introduction to Macaulay2
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Benchmark -- standard Macaulay2 benchmarks
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Bertini -- interface to Bertini
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BGG -- Bernstein-Gelfand-Gelfand correspondence
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BIBasis -- involutive Pommaret basis in a Boolean ring
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BinomialEdgeIdeals -- binomial edge ideals
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Binomials -- specialized routines for binomial ideals
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BoijSoederberg -- betti diagram operations useful for investigating the Boij-Soederberg conjectures
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Book3264Examples -- examples to accompany the eponymous book by Eisenbud and Harris
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BooleanGB -- Groebner bases for ideals in Boolean polynomial quotient rings
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Browse -- a method for browsing and examining Macaulay2 data structures
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Bruns -- make a 3-generator ideal with an "any" resolution
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ChainComplexExtras -- some additional ChainComplex Functions
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ChainComplexOperations -- sym2, wedge2, chi2 of a ChainComplex
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CharacteristicClasses -- CSM classes, Segre classes and the Euler characteristic for some subschemes of smooth complete toric varieties
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Chordal -- routines that exploit chordal structure
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Classic -- a classic Macaulay parser
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CohomCalg -- interface to CohomCalg software for computing cohomology of torus invariant divisors on a toric variety
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CoincidentRootLoci -- coincident root loci
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CompleteIntersectionResolutions -- Analyzing Resolutions over a Complete Intersection
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Complexes -- development package for beta testing new version of chain complexes
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ConformalBlocks -- for conformal block divisors
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ConvexInterface -- interface to Convex
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ConwayPolynomials -- a database of Conway polynomials
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CorrespondenceScrolls -- correspondence scrolls
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Cremona -- rational maps between projective varieties
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Cyclotomic -- cyclotomic fields
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DecomposableSparseSystems -- Solving decomposable sparse systems
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Depth -- aids in computations related to depth
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DeterminantalRepresentations -- determinantal representations
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DGAlgebras -- data type for DG algebras
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DiffAlg -- specialized routines for differential forms
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Divisor -- Weil divisors
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Dmodules -- D-modules
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EdgeIdeals -- edge ideals
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Elimination -- elimination of variables
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EliminationMatrices -- resultants
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EllipticCurves -- group law on elliptic curves (and counting points with brute force methods)
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EllipticIntegrals -- uniformization of elliptic curves
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EngineTests -- a test suite for the Macaulay2 engine
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EnumerationCurves -- Enumeration of rational curves via torus actions
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EquivariantGB -- Equivariant Groebner bases and related algorithms
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ExampleSystems -- database of polynomial systems
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ExteriorIdeals -- monomial ideals over exterior algebras
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FastLinAlg -- A package for faster linear algebra operations.
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FGLM -- Groebner bases via the FGLM algorithm
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FiniteFittingIdeals -- Fitting ideals of finite modules
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FirstPackage -- an example Macaulay2 package
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FormalGroupLaws -- commutative formal group laws
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FourierMotzkin -- convex hulls and polar cones
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FourTiTwo -- Interface to 4ti2
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FrobeniusThresholds -- F-thresholds
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GenericInitialIdeal -- find the generic initial ideal of a given ideal
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gfanInterface -- interface to Anders Jensen's Gfan software
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GradedLieAlgebras -- computations in graded Lie algebras
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GraphicalModels -- discrete and Gaussian graphical models
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Graphics -- create graphics
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Graphs -- graphs and directed graphs (digraphs)
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GroebnerWalk -- Groebner bases via the Groebner walk
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HigherCIOperators -- higher CI operators
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HighestWeights -- decompose free resolutions and graded modules with a semisimple Lie group action
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HodgeIntegrals -- Hodge integrals on the moduli space of curves
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HyperplaneArrangements -- hyperplane arrangements
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IntegralClosure -- integral closure
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InvariantRing -- construct the invariant ring of a finite group
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InverseSystems -- equivariant Macaulay inverse systems
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InvolutiveBases -- Methods for Janet bases and Pommaret bases in Macaulay 2
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K3Carpets -- K3 double structure on scrolls
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Kronecker -- Kronecker and rational normal forms
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KustinMiller -- unprojection and the Kustin-Miller complex construction
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LatticePolytopes -- lattice polytopes
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LexIdeals -- lexicographic-type monomial ideals
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Licenses -- licensing of Macaulay2
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LieTypes -- common types for Lie groups and Lie algebras
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LLLBases -- Lenstra-Lenstra-Lovasz bases
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LocalRings -- operations over a local ring (R, P)
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M0nbar -- calculations for divisors and F-curves on the moduli space of stable n-pointed genus zero curves
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MapleInterface -- interface to Maple
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Markov -- Markov ideals arising from Bayesian networks in statistics
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Matroids -- a package for computations with matroids
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MCMApproximations -- MCM approximations and complete intersections
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MinimalPrimes -- minimal primes of an ideal
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Miura -- arithmetic of Miura curves
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MixedMultiplicity -- Mixed Multiplicities of ideals
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ModuleDeformations -- versal deformations of maximal Cohen-Macaulay modules
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MonodromySolver -- solving polynomial systems via monodromy
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MonomialAlgebras -- monomial algebras
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MultiGradedRationalMap -- degree and birationality of multi-graded rational maps
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MultiplierIdeals -- multiplier ideals, log canonical thresholds, and jumping numbers
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MultiplierIdealsDim2 -- multiplier ideals in 2-dimensional rings
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NAGtypes -- types used in Numerical Algebraic Geometry
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Nauty -- interface to nauty
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NautyGraphs -- interface to nauty (Graphs fork)
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NCAlgebra -- data types for noncommutative algebras
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NoetherNormalization -- place an ideal in Noether normal position
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NonminimalComplexes -- non-minimal strands of a non-minimal resolution of a homogeneous module
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Normaliz -- interface to Normaliz in Macaulay2
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NormalToricVarieties -- routines for working with normal toric varieties and related objects
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NumericalAlgebraicGeometry -- numerical algebraic geometry
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NumericalCertification -- numerical certification
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NumericalHilbert -- numerically compute local dual space and Hilbert functions
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NumericalImplicitization -- numerical invariants of images of varieties
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NumericalSchubertCalculus -- numerical methods in Schubert Calculus
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NumericSolutions -- solving systems of polynomial equalities
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OldPolyhedra -- convex polyhedra
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OldToricVectorBundles -- vector bundles on toric varieties
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OpenMath -- OpenMath for Macaulay2
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PackageCitations -- citation of Macaulay2 packages
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PackageTemplate -- an example Macaulay2 package
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Parametrization -- rational parametrization of rational plane curves and related computations
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Parsing -- a framework for creating recursive descent parsers
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PencilsOfQuadrics -- Clifford Algebra of a pencil of quadratic forms
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Permanents -- permanents of a matrix
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PHCpack -- interface to PHCpack
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PhylogeneticTrees -- invariants for group-based phylogenetic models
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PieriMaps -- maps between representations of the general linear group based on the Pieri formulas
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Points -- sets of points
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Polyhedra -- convex polyhedra
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Polymake -- interfacing with polymake
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Posets -- partially ordered sets (posets)
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PositivityToricBundles -- check positivity of toric vector bundles
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PrimaryDecomposition -- functions for primary decomposition
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PruneComplex -- pruning chain complexes over polynomial and local rings
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Pullback -- pullback of rings
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PushForward -- push forwards of finite ring maps
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QthPower -- An implementation of the Qth-Power algorithm for computing integral closures
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Quasidegrees -- quasidegrees and graded local cohomology
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QuillenSuslin -- the Quillen-Suslin algorithm for bases of projective modules
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RandomCanonicalCurves -- Construction of random smooth canonical curves up to genus 14
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RandomComplexes -- random complexes over fields or the integers
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RandomCurves -- random curves
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RandomCurvesOverVerySmallFiniteFields -- general canonical curves of genus <= 15 over fields with small characteristic
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RandomGenus14Curves -- random smooth curves of genus 14
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RandomIdeals -- creating random ideals of various sorts
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RandomMonomialIdeals -- Erdos-Renyi-type random monomial ideals
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RandomObjects -- a framework for making random objects in algebraic geometry
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RandomPlaneCurves -- random plane curves
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RandomSpaceCurves -- random smooth space curves
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RationalMaps -- rational maps
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RationalPoints -- find the common zeroes of a set of polynomials with coefficients in a finite field
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ReactionNetworks -- reaction networks
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ReesAlgebra -- Rees algebras
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ReflexivePolytopesDB -- simple access to Kreuzer-Skarke database of reflexive polytopes of dimensions 3 and 4
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Regularity -- Castelnuovo-Mumford regularity of a homogeneous ideal
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RelativeCanonicalResolution -- the relative canonical resolution for g-nodal canonical curves with a fixed g^1_k
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ResidualIntersections -- conditions associated to residual intersection theory
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Resultants -- resultants, discriminants, and Chow forms
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RunExternalM2 -- run Macaulay2 functions outside the current Macaulay2 process
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Schubert2 -- characteristic classes for varieties without equations
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SchurComplexes -- Schur functors of complexes
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SchurFunctors -- Schur modules and maps between them
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SchurRings -- representation rings of general linear groups and of symmetric groups
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SCSCP -- SCSCP for Macaulay2
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SectionRing -- the section ring of a Weil Divisor
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SegreClasses -- test containment of varieties and computes algebraic multiplicity of subvarieties and Fulton-MacPherson intersection products, via a very general Segre class computation
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SemidefiniteProgramming -- semidefinite programming
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Seminormalization -- seminormalization of rings
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Serialization -- reversible conversion of all Macaulay2 objects to strings
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SimpleDoc -- a simple documentation function
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SimplicialComplexes -- simplicial complexes
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SimplicialDecomposability -- various decomposability routines for simplicial complexes
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SimplicialPosets -- Package for constructing Stanley simplicial poset rings.
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SlackIdeals -- Slack ideals of polytopes and matroids
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SLnEquivariantMatrices -- file ancillary to the paper "A construction of equivariant bundles on the space of symmetric forms"
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SLPexpressions -- straight line programs and algebraic circuits
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SpaceCurves -- space curves
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SparseResultants -- computations with sparse resultants
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SpechtModule -- invariants for permutation groups
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SpecialFanoFourfolds -- special cubic fourfolds and special Gushel-Mukai fourfolds
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SpectralSequences -- spectral sequences
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SRdeformations -- deformations of Stanley-Reisner rings and related computations
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StatePolytope -- the state polytope of an ideal
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StronglyStableIdeals -- studying strongly stable ideals related to Hilbert polynomials
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Style -- style sheets and images for the documentation
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SumsOfSquares -- sums of squares
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SVDComplexes -- SVD (singular value decomposition) of a complex over the reals and related functions
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SymbolicPowers -- symbolic powers
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SymmetricPolynomials -- symmetric polynomials
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TangentCone -- tangent cones
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TateOnProducts -- Tate resolutions on products of projective spaces
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TensorComplexes -- multilinear algebra with labeled bases
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TestIdeals -- singularities in positive characteristic
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Text -- documentation and hypertext
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ThreadedGB -- Compute a Groebner basis using the classical Buchberger with multiple threads
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Topcom -- interface to a small part of topcom
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TorAlgebra -- classification of local rings based on multiplication in homology
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ToricInvariants -- Euclidean distance degrees, polar degrees, degree and codimension of the dual, and Chern-Mather classes of toric varieties X_A from the polytope conv(A) or from its Gale dual
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ToricTopology -- toric topology
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ToricVectorBundles -- vector bundles on toric varieties
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TriangularSets -- triangular decompositions of ideals
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Triplets -- triplets of degree sequences and associated Betti diagrams and cohomology tables
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Tropical -- tropical geometry
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Truncations -- truncation of a module
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Units -- units conversion and physical constants
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VectorFields -- vector fields
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VectorGraphics -- A package to produce SVG graphics
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VersalDeformations -- versal deformations and local Hilbert schemes
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VirtualResolutions -- Methods for virtual resolutions on products of projective spaces
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Visualize -- interactive visualization and manipulation of combinatorial objects in a browser
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WeylGroups -- root systems and Weyl groups
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XML -- an XML parser