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1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
1 This file provides documentation for modules in Biopython that have been moved
2 or deprecated in favor of other modules. This provides some quick and easy
3 to find documentation about how to update your code to work again.
4
b4379ed @peterjc Dropping support for Python 2.3
peterjc authored
5 Python 2.3
6 ==========
7 No longer supported as of Release 1.51, having triggered a warning with
8 Release 1.50, with a mention in the release notes for Release 1.49.
9
1b8c00f @peterjc Deprecating psycopg support in BioSQL code (use psycopg2 instead)
peterjc authored
10 BioSQL and psycopg
11 ==================
12 Support for psycopg (version one) in Biopython's BioSQL code was deprecated
13 in Release 1.51, please use psycopg2 instead.
14
2e2a26b @peterjc Declare Bio.Application.generic_run and ApplicationResult obsolete
peterjc authored
15 Bio.Application.generic_run and ApplicationResult
16 =================================================
17 Declared obsolete in Release 1.51, please use Python subprocess module instead.
18
68d63b1 @peterjc Use of rettype='genbank' in Entrez EFetch (Bug 2811)
peterjc authored
19 Bio.Entrez.efetch and rettype="genbank"
20 =======================================
21 As of Easter 2009, the NCBI have stopped supporting the unofficial return type
22 of "genbank" in EFetch. Instead we should be using "gb" (GenBank) or "gp"
23 (GenPept). Bio.Entrez.efetch will correct this automatically, but issues a
24 deprecation warning.
25
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
26 Bio.SwissProt.SProt
27 ===================
604b42d Deprecating Bio.SwissProt.SProt, as its tasks have been taken over by
mdehoon authored
28 Declared obsolete in Release 1.50, and deprecated for Release 1.51. Most of the
29 functionality in Bio.SwissProt.SProt is available from Bio.SwissProt. Bio.SeqIO
30 currently uses Bio.SwissProt instead of Bio.SwissProt.SProt to parse SwissProt
31 files.
04a070a Adding deprecation information for Bio.SwissProt.SProt.
mdehoon authored
32
60fa8b7 Declaring Bio.Enzyme obsolete in favor of Bio.ExPASy.Enzyme.
mdehoon authored
33 Bio.Prosite and Bio.Enzyme
34 ==========================
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
35 Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
04dcf21 @peterjc Minor correction to new module name
peterjc authored
36 Most of the functionality has moved to Bio.ExPASy.Prosite and
37 Bio.ExPASy.Enzyme, respectively.
14901ca @peterjc Bio.Prosite is obsolete
peterjc authored
38
4bb3510 @peterjc Declaring the Bio.NetCatch and Bio.FilteredReader modules, and the Bi…
peterjc authored
39 Bio.EZRetrieve, Bio.NetCatch, Bio.File.SGMLHandle, Bio.FilteredReader
40 =====================================================================
2f3a9a6 @peterjc Declaring Bio.EZRetrieve obsolete (see mailing list)
peterjc authored
41 Declared obsolete in Release 1.50, will be deprecated in a subsequent release.
42
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
43 Bio.Graphics.GenomeDiagram and colour/color, centre/center
44 ==========================================================
45 GenomeDiagram originally used colour and centre (UK spelling of color and
46 center) for argument names. As part of its integration into Biopython 1.50,
47 this will support both colour and color, and both centre and center, to help
48 people port existing scripts written for the standalone version of
49 GenomeDiagram. However, we do intend to deprecate and then eventually
50 remove support for colour and centre in later releases of Biopython.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
51
52 Bio.AlignAce and Bio.MEME
53 =========================
54 As of Biopython 1.50, these modules are considered to be obsolete with the
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
55 introduction of Bio.Motif, and they will be deprecated in a future release.
9a188e0 @peterjc Colour/color support (mostly comment changes, but a couple of codes c…
peterjc authored
56
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
57 Numeric support
58 ===============
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
59 Following the release of 1.48, Numeric support in Biopython is discontinued.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
60 Please move to NumPy for Biopython 1.49 or later.
2669c4d - Updates to move from Numeric python to NumPy. Python modules have b…
chapmanb authored
61
b1fcca3 @peterjc Centre/center in GenomeDiagram
peterjc authored
62 Bio.Seq and the data property
63 =============================
64 Direct use of the Seq object (and MutableSeq object) .data property is
65 discouraged. As of release 1.49, writing to the Seq object's .data property
66 triggers a warning, and this property is likely to be made read only in the
67 next release.
cfd18f5 @peterjc Making the Seq object's .data into a new style property with a warnin…
peterjc authored
68
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
69 Bio.Transcribe and Bio.Translate
70 ================================
83765c0 @peterjc Deprecating Bio.Translate and Bio.Transcribe which were declared obso…
peterjc authored
71 Declared obsolete in Release 1.49, deprecated in Release 1.51.
41a4497 @peterjc Declaring Bio.Transcribe and Bio.Translate as obsolete and likely to …
peterjc authored
72 Please use the methods or functions in Bio.Seq instead.
73
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
74 Bio.mathfns, Bio.stringfns and Bio.listfns (and their C code variants)
75 ==========================================
76 Declared obsolete in Release 1.49.
8b4babf @peterjc Deprecating Bio.mathfns and Bio.stringfns
peterjc authored
77 Bio.mathfns and Bio.stringfns were deprecated in Release 1.50
78 (the deprecation of Bio.listfns is still pending)
1255664 @peterjc Declaring Bio.mathfns, Bio.stringfns, Bio.listfns and their C impleme…
peterjc authored
79
04cfde9 @peterjc Mention Bio.distance deprecation and Bio.cdistance removal (see Bug 2…
peterjc authored
80 Bio.distance (and Bio.cdistance)
81 ================================
82 Bio.distance was deprecated in Release 1.49, at which point its C code
83 implementation Bio.cdistance was removed (this was not intended as a public
84 API).
85
db96eda @peterjc Deprecating Bio.Ndb as the website this parsed has been redesigned.
peterjc authored
86 Bio.Ndb
87 =======
88 Deprecated in Release 1.49, as the website this parsed has been redesigned.
89
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
90 Martel
91 ======
f91db85 @peterjc Finished removing Martel and modules dependent on it.
peterjc authored
92 Declared obsolete in Release 1.48, deprecated in Release 1.49, and removed
93 in Release 1.51. The source code for Martel is still in our repository if
94 anyone wanted to develop this outside of Biopython.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
95
83ff4ce @peterjc Update DEPRECATED file now that Bio.Mindy etc has been removed
peterjc authored
96 Bio.Mindy and associated modules.
97 =================================
98 Declared obsolete in Release 1.48, deprecated in Release 1.49, removed in
99 Release 1.51. This includes the Bio.Writer, Bio.writers, Bio.builders,
100 Bio.Std, Bio.StdHandler, Bio.Decode and Bio.DBXRef modules
fd2e06b @peterjc Adding minimal module docstrings for the deprecated Bio.Writers/Bio.w…
peterjc authored
101
2aa69ce @peterjc Deprecating Bio.Fasta module (see mailing list)
peterjc authored
102 Bio.Fasta index_file and Dictionary
103 ===================================
104 Deprecated in Release 1.44, removed in Biopython 1.46. For small to medium
105 sized files, use Bio.SeqIO.to_dict() to make an in memory dictionary of
106 SeqRecord objects instead.
107
108 Bio.Fasta (including Bio.Fasta.FastaAlign)
109 ==========================================
110 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
111 Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead.
112
39c456c @peterjc Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…
peterjc authored
113 Bio.Align.FormatConvert
114 =======================
115 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
116 Please use Bio.AlignIO or the Alignment object's format method instead.
117
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
118 Bio.Emboss.Primer
119 =================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
120 Deprecated in Release 1.48, this parser was replaced by Bio.Emboss.Primer3
121 and Bio.Emboss.PrimerSearch instead.
6ce5052 @peterjc Bio.Emboss.Primer was deprecated in Biopython 1.48
peterjc authored
122
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
123 Bio.MetaTool
124 ============
02ac9db @peterjc Removing deprecated Martel dependent module Bio.MetaTool
peterjc authored
125 Deprecated in Release 1.48, and removed in Release 1.51, this was a parser
126 for the output of MetaTool 3.5 which is now obsolete.
fb76593 @peterjc Labelling Martel and Bio.Mindy as obsolete, updating the news about t…
peterjc authored
127
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
128 Bio.GenBank
129 ===========
130 The online functionality (search_for, download_many, and NCBIDictionary) was
5b78a4e @peterjc Deprecating the online bits of Bio.GenBank in favour of Bio.Entrez (t…
peterjc authored
131 declared obsolete in Release 1.48, and deprecated in Release 1.50.
132 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
133
134 Bio.PubMed
135 ==========
558b4c0 @peterjc Deprecating Bio.PubMed in favour of Bio.Entrez
peterjc authored
136 Declared obsolete in Release 1.48, deprecated in Release 1.49.
137 Please use Bio.Entrez instead.
81015eb @peterjc Declaring Bio.PubMed and the online parts of Bio.GenBank as OBSOLETE,…
peterjc authored
138
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
139 Bio.EUtils
140 ==========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
141 Deprecated in favor of Bio.Entrez in Release 1.48.
01e6e76 @peterjc Bio.EUtils deprecated in favour of Bio.Entrez
peterjc authored
142
4796600 @peterjc Noting API change for Bio.Sequencing
peterjc authored
143 Bio.Sequencing
144 ==============
145 A revised API was added and the old one deprecated in Biopython 1.48:
146 Bio.Sequencing.Ace.RecordParser --> Bio.Sequencing.Ace.read(handle)
147 Bio.Sequencing.Ace.Iterator --> Bio.Sequencing.Ace.parse(handle)
148 Bio.Sequencing.Phd.RecordParser --> Bio.Sequencing.Phd.read(handle)
149 Bio.Sequencing.Phd.Iterator --> Bio.Sequencing.Phd.parse(handle)
150
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
151 Bio.Blast.NCBIWWW
152 =================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
153 The HTML BLAST parser was deprecated as of Release 1.48.
154 The deprecated functions blast and blasturl were removed in Release 1.44.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
155
156 Bio.Saf
157 =======
56321cf @peterjc Removing deprecated Martel dependent module Bio.Saf
peterjc authored
158 Deprecated as of Release 1.48, removed in Release 1.51. If useful, a parser
159 for this "simple alignment format" could be developed for Bio.AlignIO instead.
fa7ab2d @peterjc Updating for recent deprecations
peterjc authored
160
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
161 Bio.NBRF
162 ========
585ac9c @peterjc Removing deprecated Martel dependent module Bio.NBRF
peterjc authored
163 Deprecated as of Release 1.48 in favor of the "pir" format in Bio.SeqIO,
164 removed in Release 1.51.
ad46521 @peterjc Deprecating Bio.NBRF in favour of the 'pir' format in Bio.SeqIO
peterjc authored
165
5be4221 @peterjc Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO
peterjc authored
166 Bio.IntelliGenetics
167 ===================
986a399 @peterjc Removing deprectaed Martel dependent module Bio.Intelligenetics
peterjc authored
168 Deprecated as of Release 1.48 in favor of the "ig" format in Bio.SeqIO,
169 removed in Release 1.51.
d01c450 Getting ready for release 1.46.
mdehoon authored
170
890dada @peterjc Removing deprecated Bio.SeqIO submodules (code was moved under Bio.Al…
peterjc authored
171 Bio.SeqIO submodules PhylipIO, ClustalIO, NexusIO and StockholmIO
172 =================================================================
173 You can still use the "phylip", "clustal", "nexus" and "stockholm" formats
174 in Bio.SeqIO, however these are now supported via Bio.AlignIO, with the
175 old code deprecated in Releases 1.46 or 1.47, and removed in Release 1.49.
176
5e507c9 Updating for release 1.47.
mdehoon authored
177 Bio.ECell
178 =========
179 Deprecated as of Release 1.47, as it appears to have no users, and the code
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
180 does not seem relevant for ECell 3. Removed in Release 1.49.
5e507c9 Updating for release 1.47.
mdehoon authored
181
d4f785b @peterjc Removing Bio.Ais which was deprecated in Biopython 1.45
peterjc authored
182 Bio.Ais
183 =======
184 Deprecated as of Release 1.45, removed in Release 1.49.
185
3f5ba50 @peterjc Removing Bio.LocusLink which was deprecated in Biopython 1.45 -- the …
peterjc authored
186 Bio.LocusLink
187 =============
188 Deprecated as of Release 1.45, removed in Release 1.49.
189 The NCBI's LocusLink was superseded by Entrez Gene.
190
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
191 Bio.SGMLExtractor
192 =================
193 Deprecated as of Release 1.46, removed in Release 1.49.
194
d01c450 Getting ready for release 1.46.
mdehoon authored
195 Bio.Rebase
196 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
197 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
198
199 Bio.Gobase
200 ==========
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
201 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
202
203 Bio.CDD
204 =======
edb3ac6 @peterjc Removing modules Bio.SGMLExtractor, Bio.CDD, Bio.Gobase and Bio.Rebas…
peterjc authored
205 Deprecated as of Release 1.46, removed in Release 1.49.
d01c450 Getting ready for release 1.46.
mdehoon authored
206
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
207 Bio.biblio
208 ==========
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
209 Deprecated as of Release 1.45, removed in Release 1.48
21059b1 @peterjc Bio.biblio was deprecated for Biopython 1.45, but I didn't remember t…
peterjc authored
210
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
211 Bio.WWW
212 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
213 The modules under Bio.WWW were deprecated in Release 1.45, and removed in
214 Release 1.48. The remaining stub Bio.WWW was deprecated in Release 1.48.
b927439 @peterjc Bio.WWW deprecation, and updating old entries to say when they were r…
peterjc authored
215
4556db2 @peterjc Bringing these up to date with changes since Biopython 1.44
peterjc authored
216 The functionality in Bio.WWW.SCOP, Bio.WWW.InterPro and Bio.WWW.ExPASy
217 is now available from Bio.SCOP, Bio.InterPro and Bio.ExPASy instead.
218
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
219 Bio.SeqIO
220 =========
221 The old Bio.SeqIO.FASTA and Bio.SeqIO.generic were deprecated in favour of
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
222 the new Bio.SeqIO module as of Release 1.44, removed in Release 1.47.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
223
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
224 Bio.Medline.NLMMedlineXML
225 =========================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
226 Deprecated in Release 1.44, removed in 1.46.
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
227
228 Bio.MultiProc
229 =============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
230 Deprecated in Release 1.44, removed in 1.46.
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
231
232 Bio.MarkupEditor
233 ================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
234 Deprecated in Release 1.44, removed in 1.46.
fe10992 @peterjc Mentioning a few old modules deprecated in 1.44 and removed in 1.46
peterjc authored
235
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
236 Bio.lcc
237 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
238 Deprecated in favor of Bio.SeqUtils.lcc in Release 1.44, removed in 1.46.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
239
240 Bio.crc
241 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
242 Deprecated in favor of Bio.SeqUtils.CheckSum in Release 1.44, removed in 1.46.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
243
244 Bio.FormatIO
245 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
246 This was removed in Release 1.44 (a deprecation was not possible).
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
247
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
248 Bio.expressions, Bio.config, Bio.dbdefs, Bio.formatdefs and Bio.dbdefs
249 ======================================================================
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
250 These were deprecated in Release 1.44, and removed in Release 1.49.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
251
252 Bio.Kabat
253 =========
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
254 This was deprecated in Release 1.43 and removed in Release 1.44.
5145a4d @peterjc Bringing this up to date for Biopython 1.44
peterjc authored
255
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
256 Bio.SeqUtils
257 ============
258 The functions 'complement' and 'antiparallel' in Bio.SeqUtils have been
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
259 deprecated as of Release 1.31, and removed in Release 1.43.
260 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
34b4f31 Added the functions 'complement' and 'reverse_complement' to Bio.Seq'…
mdehoon authored
261
262 Bio.GFF
263 =======
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
264 The functions 'forward_complement' and 'antiparallel' in Bio.GFF.easy have
265 been deprecated as of Release 1.31, and removed in Release 1.43.
76300d6 @peterjc Updates include deprecation of Martel/Mindy
peterjc authored
266 Use the functions 'complement' and 'reverse_complement' in Bio.Seq instead.
efd9b60 Added blast to qblast change to DEPRECATED file
chapmanb authored
267
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
268 Bio.sequtils
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
269 ============
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
270 Deprecated as of Release 1.30, removed in Release 1.42.
1c02f0c Bio.sequtils and Bio.SeqUtils were duplicated code, and even worse we…
chapmanb authored
271 Use Bio.SeqUtils instead.
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
272
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
273 Bio.SVM
274 =======
bbfff83 @peterjc Removing Bio.ECell which was deprecated in Biopython 1.47 (also added…
peterjc authored
275 Deprecated as of Release 1.30, removed in Release 1.42.
909bae9 Deprecated Bio.SVM and recommend usage of libsvm.
chapmanb authored
276 The Support Vector Machine code in Biopython has been superceeded by a
277 more robust (and maintained) SVM library, which includes a python
278 interface. We recommend using LIBSVM:
279
280 http://www.csie.ntu.edu.tw/~cjlin/libsvm/
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
281
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
282 Bio.RecordFile
283 ==============
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
284 Deprecated as of Release 1.30, removed in Release 1.42. RecordFile wasn't
285 completely implemented and duplicates the work of most standard parsers.
23b046b Removed internal references to RecordFile, which are really not needed.
chapmanb authored
286
b0acc00 Added instructions on how to move to Bio.Cluster from Bio.kMeans and
mdehoon authored
287 Bio.kMeans and Bio.xkMeans
288 ==========================
4b3e68b @peterjc Adjusting some line breaks. Removed the long section on moving from …
peterjc authored
289 Deprecated as of Release 1.30, removed in Release 1.42. Instead, please use
290 the function kcluster in Bio.Cluster which performs k-means or k-medians
291 clustering.
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