update the manual with bound_pop for newest release

smithlabcode · Oct 29, 2015 · 0f85f47 · 0f85f47
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diff --git a/docs/RELEASE_NOTES.txt b/docs/RELEASE_NOTES.txt
@@ -1,3 +1,14 @@
+preseq beta release 2.0.0 (October 29, 2014)
+
+------------------------------------------------------------------
+
+Notable changes in preseq software:
+
+  * Include the module bound_pop.  This module constructs a 
+    nonparametric moment-based estimator of species richness,
+    the total number of species or classes in the population.
+
+
 preseq beta release 1.0.3 (December 15, 2014)
 
 ------------------------------------------------------------------

diff --git a/docs/TCR_richness_vs_age_lm.pdf b/docs/TCR_richness_vs_age_lm.pdf
diff --git a/docs/biblio.bib b/docs/biblio.bib
@@ -1,3 +1,43 @@
+@article{willis2015inference,
+  title={Inference for changes in biodiversity},
+  author={Willis, Amy and Bunge, John and Whitman, Thea},
+  journal={arXiv preprint arXiv:1506.05710},
+  year={2015}
+}
+
+@article{britanova2014age,
+  title={Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling},
+  author={Britanova, Olga V and Putintseva, Ekaterina V and Shugay, Mikhail and Merzlyak, Ekaterina M and Turchaninova, Maria A and Staroverov, Dmitriy B and Bolotin, Dmitriy A and Lukyanov, Sergey and Bogdanova, Ekaterina A and Mamedov, Ilgar Z and others},
+  journal={The Journal of Immunology},
+  volume={192},
+  number={6},
+  pages={2689--2698},
+  year={2014},
+  publisher={Am Assoc Immnol}
+}
+
+@article{daley2014modeling,
+  title={Modeling genome coverage in single-cell sequencing},
+  author={Daley, Timothy and Smith, Andrew D},
+  journal={Bioinformatics},
+  pages={btu540},
+  year={2014},
+  publisher={Oxford Univ Press}
+}
+
+
+
+@article{fu2015uniform,
+  title={Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification},
+  author={Fu, Yusi and Li, Chunmei and Lu, Sijia and Zhou, Wenxiong and Tang, Fuchou and Xie, X Sunney and Huang, Yanyi},
+  journal={Proceedings of the National Academy of Sciences},
+  volume={112},
+  number={38},
+  pages={11923--11928},
+  year={2015},
+  publisher={National Acad Sciences}
+}
+
 @article{chao1987estimating,
   title={Estimating the population size for capture-recapture data with unequal catchability},
   author={Chao, Anne},

diff --git a/docs/comparing_scWGA_coverage.pdf b/docs/comparing_scWGA_coverage.pdf
diff --git a/docs/manual.pdf b/docs/manual.pdf