conquer_comparison/include_methods.mk at master · csoneson/conquer_comparison · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
comma := ,
empty :=
space := $(empty) $(empty)

## Methods run with R 3.3
MT3.3 := edgeRLRT SAMseq Wilcoxon edgeRQLF NODES NODESnofilt BPSC DESeq2 DESeq2nofilt edgeRLRTdeconv \
MASTcpm MASTcpmDetRate MASTtpm MASTtpmDetRate SCDE edgeRLRTrobust voomlimma SeuratBimod \
SeuratBimodnofilt SeuratBimodIsExpr2 SeuratTobit DESeq2census edgeRLRTcensus monoclecensus \
monocle D3E limmatrend ROTSvoom ROTScpm ROTStpm metagenomeSeq ttest monoclecount \
edgeRQLFDetRate DESeq2betapFALSE# limmatrendDetRate
## Methods run with R 3.4/Bioconductor 3.5
MT3.4 := scDD DEsingle
## Methods run with R 3.4/Bioconductor 3.6
MT3.4bc3.6 :=# zinbwaveedgeR zinbwaveDESeq2 DESeq2LRT logregLRT

## All methods
MT := $(MT3.3) $(MT3.4) $(MT3.4bc3.6)
MTc := $(subst $(space),$(comma),$(MT))

## Methods to apply to bulk RNA-seq data sets
MTbulk := edgeRLRT SAMseq Wilcoxon edgeRQLF NODES DESeq2 DESeq2nofilt edgeRLRTdeconv \
edgeRLRTrobust voomlimma limmatrend ttest
MTcbulk := $(subst $(space),$(comma),$(MTbulk))