Index

Symbols

--ambid dreem command line option dreem-vector command line option, [1] --autosect dreem command line option dreem-vector command line option, [1] --bamd dreem command line option dreem-vector command line option, [1] --bamf dreem command line option dreem-vector command line option, [1] --barcode-length dreem command line option dreem-demultiplex command line option, [1] --barcode-start dreem command line option dreem-demultiplex command line option, [1] --base_coverage dreem command line option dreem-draw command line option, [1] --batch-size dreem command line option dreem-vector command line option, [1] --bt2-contain dreem command line option dreem-align command line option, [1] --bt2-D dreem command line option dreem-align command line option, [1] --bt2-discordant dreem command line option dreem-align command line option, [1] --bt2-dovetail dreem command line option dreem-align command line option, [1] --bt2-dpad dreem command line option dreem-align command line option, [1] --bt2-end-to-end dreem command line option dreem-align command line option, [1] --bt2-gbar dreem command line option dreem-align command line option, [1] --bt2-I dreem command line option dreem-align command line option, [1] --bt2-i dreem command line option dreem-align command line option, [1] --bt2-L dreem command line option dreem-align command line option, [1] --bt2-local dreem command line option dreem-align command line option, [1] --bt2-mixed dreem command line option dreem-align command line option, [1] --bt2-no-contain dreem command line option dreem-align command line option, [1] --bt2-no-discordant dreem command line option dreem-align command line option, [1] --bt2-no-dovetail dreem command line option dreem-align command line option, [1] --bt2-no-mixed dreem command line option dreem-align command line option, [1] --bt2-no-unal dreem command line option dreem-align command line option, [1] --bt2-orient dreem command line option dreem-align command line option, [1] --bt2-R dreem command line option dreem-align command line option, [1] --bt2-score-min dreem command line option dreem-align command line option, [1] --bt2-unal dreem command line option dreem-align command line option, [1] --bt2-X dreem command line option dreem-align command line option, [1] --bv-files dreem command line option dreem-aggregate command line option, [1] --clipped dreem command line option dreem-demultiplex command line option, [1] --clust dreem command line option --cluster-off dreem command line option --clustering-file dreem command line option dreem-aggregate command line option, [1] --convergence-cutoff dreem command line option dreem-cluster command line option, [1] --coords dreem command line option dreem-draw command line option, [1] dreem-vector command line option, [1] --cut dreem command line option dreem-align command line option, [1] --cut-a1 dreem command line option dreem-align command line option, [1] --cut-a2 dreem command line option dreem-align command line option, [1] --cut-discard-trimmed dreem command line option dreem-align command line option, [1] --cut-discard-untrimmed dreem command line option dreem-align command line option, [1] --cut-e dreem command line option dreem-align command line option, [1] --cut-g1 dreem command line option dreem-align command line option, [1] --cut-g2 dreem command line option dreem-align command line option, [1] --cut-indels dreem command line option dreem-align command line option, [1] --cut-keep-trimmed dreem command line option dreem-align command line option, [1] --cut-keep-untrimmed dreem command line option dreem-align command line option, [1] --cut-m dreem command line option dreem-align command line option, [1] --cut-nextseq dreem command line option dreem-align command line option, [1] --cut-no-indels dreem command line option dreem-align command line option, [1] --cut-no-nextseq dreem command line option dreem-align command line option, [1] --cut-O dreem command line option dreem-align command line option, [1] --cut-q1 dreem command line option dreem-align command line option, [1] --cut-q2 dreem command line option dreem-align command line option, [1] --demult-off dreem command line option --demult-on dreem command line option --demulti-overwrite dreem command line option dreem-demultiplex command line option, [1] --erase-temp dreem command line option dreem-aggregate command line option, [1] dreem-align command line option, [1] dreem-vector command line option, [1] --exclude-del dreem command line option dreem-cluster command line option, [1] --exclude-gu dreem command line option dreem-cluster command line option, [1] --fasta dreem command line option dreem-aggregate command line option, [1] dreem-align command line option, [1] dreem-demultiplex command line option, [1] dreem-vector command line option, [1] --fastq1 dreem command line option dreem-align command line option, [1] dreem-demultiplex command line option, [1] --fastq12-dir dreem command line option dreem-align command line option, [1] --fastq2 dreem command line option dreem-align command line option, [1] dreem-demultiplex command line option, [1] --fastqc dreem command line option dreem-align command line option, [1] --fastqi dreem command line option dreem-align command line option, [1] --fastqi-dir dreem command line option dreem-align command line option, [1] --fastqs dreem command line option dreem-align command line option, [1] --fastqs-dir dreem command line option dreem-align command line option, [1] --flat dreem command line option dreem-draw command line option, [1] --include-del dreem command line option dreem-cluster command line option, [1] --include-gu dreem command line option dreem-cluster command line option, [1] --index-tolerance dreem command line option dreem-demultiplex command line option, [1] --inpt dreem command line option dreem-draw command line option, [1]

--library dreem command line option dreem-aggregate command line option, [1] dreem-demultiplex command line option, [1] dreem-vector command line option, [1] --log dreem command line option --max-clusters dreem command line option dreem-cluster command line option, [1] --max-iter dreem command line option dreem-cluster command line option, [1] --max-procs dreem command line option dreem-align command line option, [1] dreem-cluster command line option, [1] dreem-vector command line option, [1] --min-iter dreem command line option dreem-cluster command line option, [1] --min-phred dreem command line option dreem-vector command line option, [1] --min-reads dreem command line option dreem-cluster command line option, [1] --mismatch-tolerence dreem command line option dreem-demultiplex command line option, [1] --mp-report dreem command line option dreem-cluster command line option, [1] --mutation_fraction dreem command line option dreem-draw command line option, [1] --mutation_fraction_identity dreem command line option dreem-draw command line option, [1] --mutation_per_read_per_reference dreem command line option dreem-draw command line option, [1] --mutations_in_barcodes dreem command line option dreem-draw command line option, [1] --no-ambid dreem command line option dreem-vector command line option, [1] --no-autosect dreem command line option dreem-vector command line option, [1] --no-cut dreem command line option dreem-align command line option, [1] --no-fastqc dreem command line option dreem-align command line option, [1] --no-flat dreem command line option dreem-draw command line option, [1] --no-parallel dreem command line option dreem-align command line option, [1] dreem-vector command line option, [1] --no-rerun dreem command line option dreem-align command line option, [1] dreem-vector command line option, [1] --no-strict-pairs dreem command line option dreem-vector command line option, [1] --num-runs dreem command line option dreem-cluster command line option, [1] --out-dir dreem command line option dreem-aggregate command line option, [1] dreem-align command line option, [1] dreem-cluster command line option, [1] dreem-demultiplex command line option, [1] dreem-draw command line option, [1] dreem-vector command line option, [1] --parallel dreem command line option dreem-align command line option, [1] dreem-vector command line option, [1] --parallel-demultiplexing dreem command line option dreem-demultiplex command line option, [1] --phred-enc dreem command line option dreem-align command line option, [1] dreem-vector command line option, [1] --polya-max dreem command line option dreem-cluster command line option, [1] --primer-gap dreem command line option dreem-vector command line option, [1] --primers dreem command line option dreem-vector command line option, [1] --profile dreem command line option --qc-extract dreem command line option dreem-align command line option, [1] --qc-no-extract dreem command line option dreem-align command line option, [1] --quiet dreem command line option --rerun dreem command line option dreem-align command line option, [1] dreem-vector command line option, [1] --rnastructure-deltag-ensemble dreem command line option dreem-aggregate command line option, [1] --rnastructure-dms-max-paired-value dreem command line option dreem-aggregate command line option, [1] --rnastructure-dms-min-unpaired-value dreem command line option dreem-aggregate command line option, [1] --rnastructure-fold-args dreem command line option dreem-aggregate command line option, [1] --rnastructure-path dreem command line option dreem-aggregate command line option, [1] --rnastructure-use-dms dreem command line option dreem-aggregate command line option, [1] --rnastructure-use-temp dreem command line option dreem-aggregate command line option, [1] --rnastructure_probability dreem command line option dreem-aggregate command line option, [1] --samples dreem command line option dreem-aggregate command line option, [1] --save-temp dreem command line option dreem-aggregate command line option, [1] dreem-align command line option, [1] dreem-vector command line option, [1] --section dreem command line option dreem-draw command line option, [1] --signal-thresh dreem command line option dreem-cluster command line option, [1] --strict-pairs dreem command line option dreem-vector command line option, [1] --temp-dir dreem command line option dreem-aggregate command line option, [1] dreem-align command line option, [1] dreem-demultiplex command line option, [1] dreem-vector command line option, [1] --verbose dreem command line option dreem-aggregate command line option, [1] --version dreem command line option -bc dreem command line option dreem-draw command line option, [1] -bv dreem command line option dreem-aggregate command line option, [1] -c dreem command line option dreem-draw command line option, [1] dreem-vector command line option, [1] -cf dreem command line option dreem-aggregate command line option, [1] -mf dreem command line option dreem-draw command line option, [1] -mfi dreem command line option dreem-draw command line option, [1] -mib dreem command line option dreem-draw command line option, [1] -mprps dreem command line option dreem-draw command line option, [1] -n dreem command line option dreem-cluster command line option, [1] -p dreem command line option dreem-vector command line option, [1] -rs dreem command line option dreem-aggregate command line option, [1] -rsa dreem command line option dreem-aggregate command line option, [1] -rsd dreem command line option dreem-aggregate command line option, [1] -rsdmax dreem command line option dreem-aggregate command line option, [1] -rsdmin dreem command line option dreem-aggregate command line option, [1] -rspa dreem command line option dreem-aggregate command line option, [1] -rspr dreem command line option dreem-aggregate command line option, [1] -rst dreem command line option dreem-aggregate command line option, [1] -v dreem command line option dreem-aggregate command line option, [1] -z dreem command line option dreem-vector command line option, [1]

B

base_coverage() (in module dreem.draw.study.Study)

C

compare_mutation_profiles() (in module dreem.draw.study.Study)

D

deltaG_vs_sub_rate() (in module dreem.draw.study.Study) dreem command line option --ambid --autosect --bamd --bamf --barcode-length --barcode-start --base_coverage --batch-size --bt2-contain --bt2-D --bt2-discordant --bt2-dovetail --bt2-dpad --bt2-end-to-end --bt2-gbar --bt2-I --bt2-i --bt2-L --bt2-local --bt2-mixed --bt2-no-contain --bt2-no-discordant --bt2-no-dovetail --bt2-no-mixed --bt2-no-unal --bt2-orient --bt2-R --bt2-score-min --bt2-unal --bt2-X --bv-files --clipped --clust --cluster-off --clustering-file --convergence-cutoff --coords --cut --cut-a1 --cut-a2 --cut-discard-trimmed --cut-discard-untrimmed --cut-e --cut-g1 --cut-g2 --cut-indels --cut-keep-trimmed --cut-keep-untrimmed --cut-m --cut-nextseq --cut-no-indels --cut-no-nextseq --cut-O --cut-q1 --cut-q2 --demult-off --demult-on --demulti-overwrite --erase-temp --exclude-del --exclude-gu --fasta --fastq1 --fastq12-dir --fastq2 --fastqc --fastqi --fastqi-dir --fastqs --fastqs-dir --flat --include-del --include-gu --index-tolerance --inpt --library --log --max-clusters --max-iter --max-procs --min-iter --min-phred --min-reads --mismatch-tolerence --mp-report --mutation_fraction --mutation_fraction_identity --mutation_per_read_per_reference --mutations_in_barcodes --no-ambid --no-autosect --no-cut --no-fastqc --no-flat --no-parallel --no-rerun --no-strict-pairs --num-runs --out-dir --parallel --parallel-demultiplexing --phred-enc --polya-max --primer-gap --primers --profile --qc-extract --qc-no-extract --quiet --rerun --rnastructure-deltag-ensemble --rnastructure-dms-max-paired-value --rnastructure-dms-min-unpaired-value --rnastructure-fold-args --rnastructure-path --rnastructure-use-dms --rnastructure-use-temp --rnastructure_probability --samples --save-temp --section --signal-thresh --strict-pairs --temp-dir --verbose --version -bc -bv -c -cf -mf -mfi -mib -mprps -n -p -rs -rsa -rsd -rsdmax -rsdmin -rspa -rspr -rst -v -z dreem-aggregate command line option --bv-files, [1] --clustering-file, [1] --erase-temp, [1] --fasta, [1] --library, [1] --out-dir, [1] --rnastructure-deltag-ensemble, [1] --rnastructure-dms-max-paired-value, [1] --rnastructure-dms-min-unpaired-value, [1] --rnastructure-fold-args, [1] --rnastructure-path, [1] --rnastructure-use-dms, [1] --rnastructure-use-temp, [1] --rnastructure_probability, [1] --samples, [1] --save-temp, [1] --temp-dir, [1] --verbose, [1] -bv, [1] -cf, [1] -rs, [1] -rsa, [1] -rsd, [1] -rsdmax, [1] -rsdmin, [1] -rspa, [1] -rspr, [1] -rst, [1] -v, [1]

dreem-align command line option --bt2-contain, [1] --bt2-D, [1] --bt2-discordant, [1] --bt2-dovetail, [1] --bt2-dpad, [1] --bt2-end-to-end, [1] --bt2-gbar, [1] --bt2-I, [1] --bt2-i, [1] --bt2-L, [1] --bt2-local, [1] --bt2-mixed, [1] --bt2-no-contain, [1] --bt2-no-discordant, [1] --bt2-no-dovetail, [1] --bt2-no-mixed, [1] --bt2-no-unal, [1] --bt2-orient, [1] --bt2-R, [1] --bt2-score-min, [1] --bt2-unal, [1] --bt2-X, [1] --cut, [1] --cut-a1, [1] --cut-a2, [1] --cut-discard-trimmed, [1] --cut-discard-untrimmed, [1] --cut-e, [1] --cut-g1, [1] --cut-g2, [1] --cut-indels, [1] --cut-keep-trimmed, [1] --cut-keep-untrimmed, [1] --cut-m, [1] --cut-nextseq, [1] --cut-no-indels, [1] --cut-no-nextseq, [1] --cut-O, [1] --cut-q1, [1] --cut-q2, [1] --erase-temp, [1] --fasta, [1] --fastq1, [1] --fastq12-dir, [1] --fastq2, [1] --fastqc, [1] --fastqi, [1] --fastqi-dir, [1] --fastqs, [1] --fastqs-dir, [1] --max-procs, [1] --no-cut, [1] --no-fastqc, [1] --no-parallel, [1] --no-rerun, [1] --out-dir, [1] --parallel, [1] --phred-enc, [1] --qc-extract, [1] --qc-no-extract, [1] --rerun, [1] --save-temp, [1] --temp-dir, [1] dreem-cluster command line option --convergence-cutoff, [1] --exclude-del, [1] --exclude-gu, [1] --include-del, [1] --include-gu, [1] --max-clusters, [1] --max-iter, [1] --max-procs, [1] --min-iter, [1] --min-reads, [1] --mp-report, [1] --num-runs, [1] --out-dir, [1] --polya-max, [1] --signal-thresh, [1] -n, [1] dreem-demultiplex command line option --barcode-length, [1] --barcode-start, [1] --clipped, [1] --demulti-overwrite, [1] --fasta, [1] --fastq1, [1] --fastq2, [1] --index-tolerance, [1] --library, [1] --mismatch-tolerence, [1] --out-dir, [1] --parallel-demultiplexing, [1] --temp-dir, [1] dreem-draw command line option --base_coverage, [1] --coords, [1] --flat, [1] --inpt, [1] --mutation_fraction, [1] --mutation_fraction_identity, [1] --mutation_per_read_per_reference, [1] --mutations_in_barcodes, [1] --no-flat, [1] --out-dir, [1] --section, [1] -bc, [1] -c, [1] -mf, [1] -mfi, [1] -mib, [1] -mprps, [1] dreem-vector command line option --ambid, [1] --autosect, [1] --bamd, [1] --bamf, [1] --batch-size, [1] --coords, [1] --erase-temp, [1] --fasta, [1] --library, [1] --max-procs, [1] --min-phred, [1] --no-ambid, [1] --no-autosect, [1] --no-parallel, [1] --no-rerun, [1] --no-strict-pairs, [1] --out-dir, [1] --parallel, [1] --phred-enc, [1] --primer-gap, [1] --primers, [1] --rerun, [1] --save-temp, [1] --strict-pairs, [1] --temp-dir, [1] -c, [1] -p, [1] -z, [1]

E

experimental_variable_across_samples() (in module dreem.draw.study.Study)

G

get_df() (in module dreem.draw.study.Study)

M

mutation_fraction() (in module dreem.draw.study.Study) mutation_fraction_delta() (in module dreem.draw.study.Study) mutation_fraction_identity() (in module dreem.draw.study.Study)

mutation_per_read_per_reference() (in module dreem.draw.study.Study) mutations_in_barcodes() (in module dreem.draw.study.Study) mutations_per_read_per_sample() (in module dreem.draw.study.Study)

N

num_aligned_reads_per_reference_frequency_distribution() (in module dreem.draw.study.Study)