alimanfoo/anhima issues and pull requests

#79 - Fix utils

Pull Request - State: open - Opened by hardingnj over 8 years ago - 2 comments

#78 - Jsfs

Pull Request - State: closed - Opened by hardingnj almost 10 years ago

#77 - PY3 support

Issue - State: closed - Opened by alimanfoo almost 10 years ago - 1 comment

#76 - locate_postion prints to console

Issue - State: closed - Opened by hardingnj almost 10 years ago - 2 comments

#75 - Add aws

Pull Request - State: closed - Opened by hardingnj almost 10 years ago - 5 comments

#74 - Multi-chromosome variant locator

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: enhancement

#73 - AN array has two dimensions but needs only one

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: usability

#72 - Samplefix

Pull Request - State: closed - Opened by hardingnj about 10 years ago - 1 comment
Labels: bug

#71 - LD plot aspect ratio

Issue - State: open - Opened by alimanfoo about 10 years ago

#70 - Improve performance of anhima.ld.ld_prune_pairwise

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: performance

#69 - Locate intervals

Issue - State: closed - Opened by alimanfoo about 10 years ago - 2 comments
Labels: enhancement, backwards-incompatible

#68 - Population ancestry likelihood

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment
Labels: enhancement

#67 - Fixed typo in chrom spec

Pull Request - State: closed - Opened by hardingnj about 10 years ago - 2 comments
Labels: bug

#66 - Adding check for basestring

Pull Request - State: closed - Opened by hardingnj about 10 years ago - 1 comment
Labels: usability

#65 - Rename take_ to view_

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: usability, backwards-incompatible

#64 - Extracting samples API flexibility

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: usability, backwards-incompatible

#63 - Use in place operations when packing/unpacking genotypes

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: performance

#62 - Axis hints in docstrings

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: documentation

#61 - Subselection routines in anhima.loc support multiple arrays

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment
Labels: wontfix, usability

#60 - Addtped

Pull Request - State: closed - Opened by hardingnj about 10 years ago - 5 comments
Labels: enhancement

#59 - Added check if a basestring

Pull Request - State: closed - Opened by hardingnj about 10 years ago - 4 comments

#58 - Impute inheritance

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: enhancement

#57 - Mendelian errors on sex chromosome

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: enhancement

#56 - Locate position, locate positions

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: enhancement

#55 - Modify pack/unpack diploid such that 0 encodes ref/ref

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: enhancement, backwards-incompatible

#54 - Bug in anhima.gt.pack_diploid for higher alleles

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: bug

#53 - Support array-like arguments throughout

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: usability

#52 - Document dependencies

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: documentation

#51 - Multiallelic Mendelian errors

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment
Labels: enhancement

#50 - Sparse genotypes

Issue - State: open - Opened by alimanfoo about 10 years ago - 1 comment
Labels: enhancement

#49 - Transform genotypes to per call allele counts

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: enhancement

#48 - Pedigree phasing

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: enhancement

#47 - Diploid Mendel errors

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: enhancement

#46 - Diploid optimisations for anhima.gt.is_het etc.

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: performance

#45 - Adding mendelian error code

Pull Request - State: closed - Opened by hardingnj about 10 years ago - 1 comment

#44 - Add option to normalise total doubleton counts by number of samples

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: enhancement

#43 - Fix alignment of total counts in anhima.f2.plot_f2_fig

Issue - State: closed - Opened by alimanfoo about 10 years ago

#42 - Option to apply variant query when loading from HDF5

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment

#41 - Drop heatmap plot of shared doubletons

Issue - State: closed - Opened by alimanfoo about 10 years ago

#40 - Break doubleton sharing functions into separate module

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment

#39 - Break site frequency spectrum functions into separate module

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment

#38 - Y limits for plotting shared doubleton counts

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment

#37 - Break apart plotting functions for shared doubleton counts

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment
Labels: enhancement

#36 - Normalise shared doubleton counts by number of distinct pairs

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment
Labels: enhancement

#35 - Write genotypes in TPED format

Issue - State: closed - Opened by alimanfoo about 10 years ago - 2 comments
Labels: enhancement

#34 - Subsample chunks (anhima.h5)

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment
Labels: enhancement

#33 - Haplotype bifurcation plots

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: enhancement

#32 - Add see also from anhima.mds functions to pairwise distance function

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: documentation

#31 - Unpack multiallelic variants

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: enhancement

#30 - Convenience functions to find fixed differences between populations and private variants

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: enhancement

#29 - Heatmap plot for distance matrix with clustering, dendrogram and row/column colour labels

Issue - State: open - Opened by alimanfoo about 10 years ago
Labels: enhancement

#28 - Tabulate inheritance switches

Issue - State: closed - Opened by alimanfoo about 10 years ago - 1 comment
Labels: enhancement

#27 - Use numpy.searchsorted instead of bisect

Issue - State: closed - Opened by alimanfoo about 10 years ago
Labels: performance

#26 - anhima.gt - is_hom and count_hom

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#25 - anhima.tree - change plot_phylo to plot to matplotlib axes

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#24 - Created ped.py

Pull Request - State: closed - Opened by hardingnj over 10 years ago

#23 - site frequency spectra

Issue - State: closed - Opened by alimanfoo over 10 years ago - 1 comment
Labels: enhancement

#22 - mpi_map_chunks (anhima.h5)

Issue - State: open - Opened by alimanfoo over 10 years ago
Labels: enhancement

#21 - Apply function over array block-wise

Issue - State: closed - Opened by alimanfoo over 10 years ago - 1 comment
Labels: enhancement

#20 - Plotting functions for variant annotations

Issue - State: open - Opened by alimanfoo over 10 years ago - 1 comment
Labels: enhancement

#19 - F statistics and Hardy Weinberg equilibrium

Issue - State: open - Opened by alimanfoo over 10 years ago - 3 comments
Labels: enhancement

#18 - Nucleotide diversity

Issue - State: open - Opened by alimanfoo over 10 years ago
Labels: enhancement

#17 - Allele balance plots

Issue - State: open - Opened by alimanfoo over 10 years ago
Labels: enhancement

#16 - f2 analyses (doubleton sharing)

Issue - State: closed - Opened by alimanfoo over 10 years ago - 1 comment
Labels: enhancement

#15 - anhima.pca - plot_variance_explained()

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#14 - anhima.pca - plot_loadings()

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#13 - anhima.mds module

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#12 - Simple plotting of genome features (genes etc.)

Issue - State: open - Opened by alimanfoo over 10 years ago
Labels: enhancement

#11 - LD decay, correct for sample size

Issue - State: open - Opened by alimanfoo over 10 years ago
Labels: bug

#10 - CNV calling utilities and diagnostics

Issue - State: open - Opened by alimanfoo over 10 years ago - 1 comment
Labels: enhancement

#9 - Plot allele frequency comparison between two populations/cohorts

Issue - State: open - Opened by alimanfoo over 10 years ago
Labels: enhancement

#8 - Pedigree utilities

Issue - State: closed - Opened by alimanfoo over 10 years ago - 4 comments
Labels: enhancement

#7 - anhima.gt - rename as_alleles() to as_haplotypes()

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#6 - anhima.loc.windowed_statistic - docstring missing return

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: documentation

#5 - Added is_gt_inconsistent function and docs

Pull Request - State: closed - Opened by hardingnj over 10 years ago - 2 comments

#4 - call np.asarray() for all array-like arguments

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: bug

#3 - anhima.tree - add support for reading and writing trees in newick format

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#2 - anhima.tree.plot_phylo() - add scale bar

Issue - State: closed - Opened by alimanfoo over 10 years ago
Labels: enhancement

#1 - minor bug fix to include highest values in a bin

Pull Request - State: closed - Opened by podpearson over 10 years ago - 6 comments

GitHub / alimanfoo/anhima issues and pull requests