dburkhardt

Hi, I just wanted to bring this back up again because I've been logging some of the issue's I've encountered. It seems we're at a bit of a philosophical divide, and so perhaps it's best for me to just register which use cases I have that AnnData / scanpy are causing me friction:

Instead of pasting all errors, I'm just going to paste code blocks I wish worked. Note, these are actual use cases I have regularly.

1. Cannot pass AnnData to numpy or sklearn operators

import scanpy as sc
import numpy as np
import pandas as pd

dburkhardt

dburkhardt

GENE 760 – Problem Set 3

The purpose of this problem set is to familiarize students with the analysis of mRNA-seq data. By the end of this problem set, you will have learned how to use:

• STAR to map spliced RNA-seq reads to a genome
• HTSeq to quantify gene expression as read counts
• DESeq2 to perform differential expression analysis
• DAVID and EnrichR to perform gene ontology analysis on a list of genes

Students are to submit a gzipped tarball called _PS3.tar.gz containing:

dburkhardt

==> Making package: parquet-cpp 1.4.0-1 (Mon 27 Aug 2018 02:17:39 PM EDT)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
  -> Found apache-parquet-cpp-1.4.0.tar.gz
==> Validating source files with sha256sums...
    apache-parquet-cpp-1.4.0.tar.gz ... Passed
==> Extracting sources...
  -> Extracting apache-parquet-cpp-1.4.0.tar.gz with bsdtar
==> Removing existing $pkgdir/ directory...