Computational Systems Biology Methods and Protocols.7z

R

Random forest (RF)......................................86,190–192,
194, 228, 250, 252, 255, 258
Random walk with restart (RWR)..............................146,
147, 150, 210, 212
Reads per kilobase per million reads mapped
(RPKM)..................................................... 22,338,
344, 352, 353
Receiver operating characteristic (ROC)............230, 381
Regulatory interaction predictor (RIP).......................191
Relative solvent accessibility (RSA)..............................226
Relevance vector machine (RVM)...............................250
Ribosomal RNA (rRNA)........................................ 15, 26,
35, 40, 168
RNA sequencing.................................................188, 311,
323, 331, 355

S

Sanger sequencing................................................. 2, 5, 47,
50, 55, 179, 390, 393, 398
Search Tool for the Retrieval of Interacting Genes/
Proteins (STRING)..................................... 76, 81,
112–114, 150
Sensitivity (SN).................................................31, 32, 38,
42, 48–50, 52, 53, 55, 59, 72, 74, 167, 190, 191,
230, 242–244, 250, 252, 254, 266, 268,
275–277, 312, 331, 376, 377, 379–381, 383,
395, 396, 401
Sequence Read Archive (SRA).....................................137
Shortest path.......................................................144, 147,
148, 150, 159, 160, 217, 226, 227, 347
Similarity network fusion (SNF) .........................122, 123
Single-cell methylome and transcriptome
sequencing (scMT-seq).....................................334
Single-cell restriction analysis of methylation
(SCRAM)...........................................................333
Single-cell RNA sequencing (scRNA-seq)........311–313,
317–324, 331, 335–337, 339, 351–358, 363
Single molecule sequencing (SMS)................................. 3,
311, 318
Single-nucleotide polymorphisms (SNPs).........7, 12, 30,
97–106, 194, 391–395, 397, 398, 400
Small Cajal body RNA (scaRNA)................................205
Small interfering RNA (siRNA)...................................205
Small nucleolar RNA (snoRNA).........................205, 210
Solvent accessible surface area (SASA)....... 224, 226, 242

Specificity (SP)........................................................ 31, 32,

38, 42, 49, 50, 53, 57, 59, 72, 191, 230, 241–243,

252, 254, 268, 277, 377, 379–381, 383, 401

Structure-toxicity relationship (STR) .........................249,

255, 256, 258, 331

Support vector machine (SVM).........................189–191,

193, 194, 224, 228, 243, 249

T

Tamias alpinus................................................................ 31

T-distributed stochastic neighbor embedding

(t-SNE)...........................169, 176, 321, 323, 324

Top-down integration........................................110, 111,

119, 122, 123, 126

Topologically associating domains (TADs).................333

Transcript per million (TPM)......................................172,

338, 348, 354, 392, 398, 399

Transcription factors (TFs).................................118, 120,

144, 191, 398

Transfer RNA (tRNA).................................................... 15

True negatives (TN)............................................230, 243

True positives (TP).....................................230, 243, 333

Tuberculous meningitis (TBM) .........................375–377,

379–383

U

Ultra-high performance liquid chromatography

(UHPLC) .................................................266, 276

Unique identifiers (UID)........................... 76, 79, 80, 84

Unique molecular identifiers (UMI)..................... 76, 90,

313, 317, 319, 336, 352, 354

V

Visual analog scale (VAS).............................................192

Voltage sensor domain (VSD)......................................256

W

Whole genome amplification (WGA) .................359, 360

X

Xenopus tropicalis............................................................ 31

Z

Ziehl–Neelsen (ZN) staining...............................376, 377

COMPUTATIONALSYSTEMSBIOLOGY:METHODS ANDPROTOCOLS

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