Loom
3.0
loompy.org
GitHub
Contents
Loompy documentation
Installation
Requirements
Easy installation
From source
Getting Started
Understanding the semantics of loom files
Connecting, not loading and saving
Reading and writing
Efficient indexing and compression
Matrix and attributes
Data types
Create from fastq
The
loompy
command-line tool
Using the
loompy
fromfq
command
API Walkthrough
Creating and connecting
Manipulate data
Cookbook
Working with a newly created file
Loading attributes from Pandas
Combining data using scan() and new()
Fitting an incremental PCA
Conventions
Single analysis per file
Orientation
Attribute naming conventions
Loom file format specs
Versions
Introduction
HDF5 concepts
Standards
Specification
Datatypes
Example
Complete API Reference
create (function)
new (function)
create_from_fastq (function)
create_from_cellranger (function)
connect (function)
combine (function)
LoomConnection (class)
LayerManager (class)
MemoryLoomLayer (class)
LoomLayer (class)
ViewManager (class)
LoomView (class)
LoomValidator (class)
Loompy documentation
Installation
Understanding the semantics of loom files
Create from fastq
API Walkthrough
Cookbook
Conventions
Loom file format specs
Complete API Reference
Index
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A
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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P
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R
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S
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V
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W
_
__init__() (loompy.LayerManager method)
(loompy.loompy.LoomConnection method)
(loompy.LoomValidator method)
(loompy.LoomView method)
(loompy.MemoryLoomLayer method)
A
add_columns() (loompy.loompy.LoomConnection method)
add_loom() (loompy.loompy.LoomConnection method)
aggregate() (loompy.loompy.LoomConnection method)
attrs (loompy.loompy.LoomConnection attribute)
C
ca (loompy.loompy.LoomConnection attribute)
close() (loompy.loompy.LoomConnection method)
closed() (loompy.loompy.LoomConnection property)
col_graphs (loompy.loompy.LoomConnection attribute)
combine() (in module loompy)
connect() (in module loompy)
create() (in module loompy)
create_from_cellranger() (in module loompy)
create_from_fastq() (in module loompy)
D
ds (loompy.LoomLayer attribute)
dtype (loompy.LoomLayer attribute)
E
errors (loompy.LoomValidator attribute)
export() (loompy.loompy.LoomConnection method)
F
filename (loompy.loompy.LoomConnection attribute)
G
get_changes_since() (loompy.loompy.LoomConnection method)
I
items() (loompy.LayerManager method)
K
keys() (loompy.LayerManager method)
L
last_modified() (loompy.LayerManager method)
(loompy.LoomLayer method)
(loompy.loompy.LoomConnection method)
LayerManager (class in loompy)
LoomConnection (class in loompy.loompy)
LoomLayer (class in loompy)
LoomValidator (class in loompy)
LoomView (class in loompy)
M
map() (loompy.LoomLayer method)
(loompy.loompy.LoomConnection method)
MemoryLoomLayer (class in loompy)
mode() (loompy.loompy.LoomConnection property)
N
name (loompy.LoomLayer attribute)
(loompy.MemoryLoomLayer attribute)
new() (in module loompy)
P
permute() (loompy.loompy.LoomConnection method)
(loompy.LoomView method)
(loompy.MemoryLoomLayer method)
R
ra (loompy.loompy.LoomConnection attribute)
row_graphs (loompy.loompy.LoomConnection attribute)
S
scan() (loompy.loompy.LoomConnection method)
shape (loompy.LoomLayer attribute)
(loompy.loompy.LoomConnection attribute)
(loompy.MemoryLoomLayer attribute)
sparse() (loompy.LoomLayer method)
(loompy.loompy.LoomConnection method)
(loompy.MemoryLoomLayer method)
summary (loompy.LoomValidator attribute)
V
validate() (loompy.LoomValidator method)
validate_conventions() (loompy.LoomValidator method)
validate_spec() (loompy.LoomValidator method)
version (loompy.LoomValidator attribute)
view (loompy.loompy.LoomConnection attribute)
ViewManager (class in loompy)
W
warnings (loompy.LoomValidator attribute)
