| $~ | Bioshake.Implicit, Bioshake |
| :-> | |
| 1 (Type/Class) | Bioshake.Types, Bioshake |
| 2 (Data Constructor) | Bioshake.Types, Bioshake |
| A | Bioshake.Types, Bioshake |
| addRGLine | |
| 1 (Function) | Bioshake.Cluster.Samtools |
| 2 (Function) | Bioshake.Samtools |
| align | |
| 1 (Function) | Bioshake.BWA |
| 2 (Function) | Bioshake.Cluster.BWA |
| All | |
| 1 (Type/Class) | Bioshake |
| 2 (Data Constructor) | Bioshake |
| allTags | Bioshake.Tags, Bioshake |
| allTransTags | Bioshake.Tags, Bioshake |
| allTransTagsPipe | Bioshake.Tags, Bioshake |
| annotate | |
| 1 (Function) | Bioshake.Cluster.SnpEff |
| 2 (Function) | Bioshake.SnpEff |
| Args | |
| 1 (Type/Class) | Bioshake.Cluster.Torque |
| 2 (Type/Class) | Bioshake.TH |
| args | |
| 1 (Function) | Bioshake.Cluster.Torque |
| 2 (Function) | Bioshake.TH |
| bedCov | |
| 1 (Function) | Bioshake.Cluster.Samtools |
| 2 (Function) | Bioshake.Samtools |
| bin | |
| 1 (Function) | Bioshake.Cluster.Sequenza |
| 2 (Function) | Bioshake.Sequenza |
| bioshake | Bioshake |
| build | Bioshake.Types, Bioshake |
| Buildable | Bioshake.Types, Bioshake |
| C | Bioshake.Types, Bioshake |
| call | |
| 1 (Function) | Bioshake.ADTEx |
| 2 (Function) | Bioshake.Cluster.ADTEx |
| 3 (Function) | Bioshake.Cluster.Platypus |
| 4 (Function) | Bioshake.Platypus |
| callSomatic | |
| 1 (Function) | Bioshake.Cluster.Varscan |
| 2 (Function) | Bioshake.Varscan |
| Capture | Bioshake |
| captureOnly | |
| 1 (Function) | Bioshake.Bedtools |
| 2 (Function) | Bioshake.Cluster.Bedtools |
| CArgs | Bioshake.TH |
| Cmd | Bioshake.TH |
| cmdArgs | |
| 1 (Function) | Bioshake.Cluster.Torque |
| 2 (Function) | Bioshake.TH |
| CmdF | |
| 1 (Type/Class) | Bioshake.TH |
| 2 (Data Constructor) | Bioshake.TH |
| cmdFinally | Bioshake.TH |
| cNVExome | |
| 1 (Function) | Bioshake.Cluster.FREEC |
| 2 (Function) | Bioshake.FREEC |
| Compilable | Bioshake.Types, Bioshake |
| compile | Bioshake.Types, Bioshake |
| Compiler | Bioshake.Types, Bioshake |
| compileRules | Bioshake.Types, Bioshake |
| Config | |
| 1 (Type/Class) | Bioshake.Cluster.Torque |
| 2 (Data Constructor) | Bioshake.Cluster.Torque |
| copyNumber | |
| 1 (Function) | Bioshake.Cluster.Varscan |
| 2 (Function) | Bioshake.Varscan |
| CPUs | Bioshake.Cluster.Torque |
| dBNSFP | |
| 1 (Function) | Bioshake.Cluster.SnpEff |
| 2 (Function) | Bioshake.SnpEff |
| dbnsfp | Bioshake |
| deDup | |
| 1 (Function) | Bioshake.Cluster.Picard |
| 2 (Function) | Bioshake.Cluster.Samtools |
| 3 (Function) | Bioshake.Picard |
| 4 (Function) | Bioshake.Samtools |
| DeDuped | Bioshake.Tags, Bioshake |
| def | Bioshake.Implicit, Bioshake |
| Default | Bioshake.Implicit, Bioshake |
| FinallyF | Bioshake.TH |
| fixMates | |
| 1 (Function) | Bioshake.Cluster.Picard |
| 2 (Function) | Bioshake.Picard |
| G | Bioshake.Types, Bioshake |
| gb | Bioshake.Cluster.Torque |
| GC | Bioshake.Cluster.Sequenza, Bioshake.Sequenza |
| getBED | Bioshake |
| getCPUs | Bioshake.Cluster.Torque |
| getGC | Bioshake.Cluster.Sequenza, Bioshake.Sequenza |
| getRef | Bioshake |
| hashPath | Bioshake.TH |
| HasRG | Bioshake.Tags, Bioshake |
| ignoringIOErrors | Bioshake |
| Implicit | Bioshake.Implicit, Bioshake |
| indexRules | Bioshake.Cluster.Samtools |
| IsBam | Bioshake.Tags, Bioshake |
| IsBcf | Bioshake.Tags, Bioshake |
| IsBed | Bioshake.Tags, Bioshake |
| IsCov | Bioshake.Tags, Bioshake |
| IsCSV | Bioshake.Tags, Bioshake |
| IsFastQ | Bioshake.Tags, Bioshake |
| IsGff | Bioshake.Tags, Bioshake |
| IsMPileup | Bioshake.Tags, Bioshake |
| IsSam | Bioshake.Tags, Bioshake |
| IsSeqzGZ | Bioshake.Tags, Bioshake |
| IsTGZ | Bioshake.Tags, Bioshake |
| IsTSV | Bioshake.Tags, Bioshake |
| IsVCF | Bioshake.Tags, Bioshake |
| makeCluster | Bioshake.TH |
| makeMultiTypes | Bioshake.TH |
| makeSingleCluster | Bioshake.TH |
| makeSingleThread | Bioshake.TH |
| makeSingleTypes | Bioshake.TH |
| makeThreaded | Bioshake.TH |
| mappedOnly | |
| 1 (Function) | Bioshake.Cluster.Samtools |
| 2 (Function) | Bioshake.Samtools |
| markDups | |
| 1 (Function) | Bioshake.Cluster.Picard |
| 2 (Function) | Bioshake.Picard |
| Mem | Bioshake.Cluster.Torque |
| MemLimit | Bioshake.TH |
| memLimit | Bioshake.TH |
| Module | Bioshake.Cluster.Torque |
| ModuleName | Bioshake.Cluster.Torque |
| name | Bioshake |
| Nuc | Bioshake.Types, Bioshake |
| out | Bioshake |
| PairedEnd | Bioshake.Tags, Bioshake |
| Param | |
| 1 (Type/Class) | Bioshake.Implicit, Bioshake |
| 2 (Data Constructor) | Bioshake.Implicit, Bioshake |
| param | Bioshake.Implicit, Bioshake |
| Pathable | Bioshake.Types, Bioshake |
| paths | Bioshake.Types, Bioshake |
| pileup | |
| 1 (Function) | Bioshake.Cluster.Samtools |
| 2 (Function) | Bioshake.Samtools |
| pileup2Seqz | |
| 1 (Function) | Bioshake.Cluster.Sequenza |
| 2 (Function) | Bioshake.Sequenza |
| Queue | |
| 1 (Data Constructor) | Bioshake.Cluster.Torque |
| 2 (Type/Class) | Bioshake.Cluster.Torque |
| Referenced | Bioshake |
| run | Bioshake.TH |
| Seq | |
| 1 (Type/Class) | Bioshake.Types, Bioshake |
| 2 (Data Constructor) | Bioshake.Types, Bioshake |
| setParam | Bioshake.Implicit, Bioshake |
| sha1 | Bioshake.TH |
| sortBam | |
| 1 (Function) | Bioshake.Cluster.Samtools |
| 2 (Function) | Bioshake.Samtools |
| Sorted | Bioshake.Tags, Bioshake |
| submit | Bioshake.Cluster.Torque |
| T | Bioshake.Types, Bioshake |
| TArgs | Bioshake.Cluster.Torque |
| Threads | |
| 1 (Type/Class) | Bioshake.Types, Bioshake |
| 2 (Data Constructor) | Bioshake.Types, Bioshake |
| TOption | Bioshake.Cluster.Torque |
| trim | |
| 1 (Function) | Bioshake.Cluster.Cutadapt |
| 2 (Function) | Bioshake.Cutadapt |
| TStdout | Bioshake.Cluster.Torque |
| Walltime | Bioshake.Cluster.Torque |
| withAll | Bioshake |
| withCmd | Bioshake.TH |
| withPair | Bioshake |
| withSubmit | Bioshake.TH |
| withTempDirectory | Bioshake |
| withTempDirectory' | Bioshake.TH |
| |-> | |
| 1 (Type/Class) | Bioshake.Cluster.Torque |
| 2 (Type/Class) | Bioshake.TH |