Index

_ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W

_

__iter__() (bbcflib.track.FeatureStream method)
__repr__() (bbcflib.genrep.GenrepObject method)

A

add() (bein.Execution method)
add_alias() (bein.MiniLIMS method)
add_and_index_bam() (in module bbcflib.mapseq)
add_bowtie_index() (in module bbcflib.mapseq)
add_group() (bbcflib.frontend.Job method)
add_macs_results() (in module bbcflib.chipseq)
add_name_field() (in module bbcflib.gfminer.common)
add_nh_flag() (in module bbcflib.mapseq)
add_pdf_stats() (in module bbcflib.mapseq)
add_pickle() (in module bein.util)
add_run() (bbcflib.frontend.Job method)
all_snps() (in module bbcflib.snp)
annot_track() (bbcflib.genrep.Assembly method), [1]
annotateBed() (in module bbcflib.gfminer.bedtools)
annotations_path (bbcflib.genrep.Assembly attribute), [1]
AnnoteFinder (class in bbcflib.maplot)
apply() (in module bbcflib.gfminer.common)
arguments (in module bein)
(ProgramOutput attribute)
assemblies_available() (bbcflib.genrep.GenRep method), [1]
assembly (bbcflib.track.Track attribute)
Assembly (class in bbcflib.genrep), [1]
assembly() (bbcflib.genrep.GenRep method), [1]
associate_file() (bein.MiniLIMS method)
associated_files_of() (bein.MiniLIMS method)

B

background() (in module bein.util)
bam_to_annot_counts() (in module bbcflib.microbiome)
bam_to_density() (in module bbcflib.mapseq)
bamstats() (in module bbcflib.mapseq)
bamToBed() (in module bbcflib.gfminer.bedtools)
bamToFastq() (in module bbcflib.gfminer.bedtools)
BamTrack (class in bbcflib.track.bin)
bbcf_valid (bbcflib.genrep.Assembly attribute), [1]
bbcflib (module)
bbcflib.c4seq (module)
bbcflib.chipseq (module)
bbcflib.common (module)
bbcflib.daflims (module)
bbcflib.demultiplex (module)
bbcflib.frontend (module)
bbcflib.gdv (module)
bbcflib.genrep (module)
bbcflib.gfminer (module)
bbcflib.gfminer.bedtools (module)
bbcflib.gfminer.common (module)
bbcflib.gfminer.numeric (module)
bbcflib.gfminer.numeric.regions (module)
bbcflib.gfminer.numeric.signal (module)
bbcflib.gfminer.stream (module)
bbcflib.gfminer.stream.annotate (module)
bbcflib.gfminer.stream.intervals (module)
bbcflib.gfminer.stream.scores (module)
bbcflib.maplot (module)
bbcflib.mapseq (module)
bbcflib.microbiome (module)
bbcflib.rnaseq (module)
bbcflib.snp (module)
bbcflib.track (module)
bbcflib.track.bin (module)
bbcflib.track.sql (module)
bbcflib.track.text (module)
bed12ToBed6() (in module bbcflib.gfminer.bedtools)
BedGraphTrack (class in bbcflib.track.text)
bedpeToBam() (in module bbcflib.gfminer.bedtools)
bedToBam() (in module bbcflib.gfminer.bedtools)
bedToIgv() (in module bbcflib.gfminer.bedtools)
BedTrack (class in bbcflib.track.text)
bein (module), [1]
bein.MiniLIMS (built-in class)
bein.util (module), [1]
BigWigTrack (class in bbcflib.track.bin)
BinTrack (class in bbcflib.track.bin)
bowtie() (in module bbcflib.mapseq)
bowtie2() (in module bbcflib.mapseq)
browse_executions() (bein.MiniLIMS method)
build_assembly() (bbcflib.genrep.Assembly method), [1]

C

c4seq_workflow() (in module bbcflib.c4seq)
camelPeaks() (in module bbcflib.chipseq)
cat() (in module bbcflib.common)
chipseq_workflow() (in module bbcflib.chipseq)
chrmeta (bbcflib.genrep.Assembly attribute), [1]
(bbcflib.track.Track attribute)
chrnames (bbcflib.genrep.Assembly attribute), [1]
chromosomes (bbcflib.genrep.Assembly attribute), [1]
closestBed() (in module bbcflib.gfminer.bedtools)
clusterBed() (in module bbcflib.gfminer.bedtools)
cobble() (in module bbcflib.gfminer.common)
column_by_name() (bbcflib.track.Track method)
combine() (in module bbcflib.gfminer.stream.intervals)
complementBed() (in module bbcflib.gfminer.bedtools)
concat_fields() (in module bbcflib.gfminer.common)
concatenate() (in module bbcflib.gfminer.stream.intervals)
connection (bbcflib.track.sql.SqlTrack attribute)
convert() (in module bbcflib.track)
copy() (in module bbcflib.gfminer.common)
copy_file() (bein.MiniLIMS method)
correlation() (in module bbcflib.gfminer.numeric.signal)
count() (bbcflib.track.bin.BamTrack method)
count_lines() (in module bein.util)
countident() (in module bbcflib.demultiplex)
coverage() (bbcflib.track.bin.BamTrack method)
coverageBed() (in module bbcflib.gfminer.bedtools)
create_exome_gtf() (bbcflib.genrep.Assembly method), [1]
create_tracks() (in module bbcflib.snp)
created_at (bbcflib.genrep.Assembly attribute), [1]
cursor (bbcflib.track.sql.SqlTrack attribute)

D

DAFLIMS (class in bbcflib.daflims), [1]
data (bbcflib.track.FeatureStream attribute)
delete_alias() (bein.MiniLIMS method)
delete_execution() (bein.bein.MiniLIMS.MiniLIMS method)
(bein.MiniLIMS method)
delete_file() (bein.bein.MiniLIMS.MiniLIMS method)
(bein.MiniLIMS method)
delete_file_association() (bein.MiniLIMS method)
densities_groups() (in module bbcflib.mapseq)
density_to_countsPerFrag() (in module bbcflib.c4seq)
disjunction() (in module bbcflib.gfminer.stream.intervals)
distance() (bbcflib.maplot.AnnoteFinder method)
drawAnnote() (bbcflib.maplot.AnnoteFinder method)
duplicate() (in module bbcflib.gfminer.common)

E

ensembl_to_ucsc() (in module bbcflib.track)
exclude() (in module bbcflib.gfminer.stream.intervals)
Execution (class in bein)
execution() (in module bein)
exon_snps() (in module bbcflib.snp)
exon_track() (bbcflib.genrep.Assembly method), [1]
expandCols() (in module bbcflib.gfminer.bedtools)
export_file() (bein.MiniLIMS method)

F

fasta_by_chrom (bbcflib.genrep.Assembly attribute), [1]
fasta_from_regions() (bbcflib.genrep.Assembly method), [1]
fasta_path() (bbcflib.genrep.Assembly method), [1]
fastaFromBed() (in module bbcflib.gfminer.bedtools)
feature_matrix() (in module bbcflib.gfminer.numeric.regions)
FeatureStream (class in bbcflib.track)
fetch_execution() (bein.bein.MiniLIMS.MiniLIMS method)
(bein.MiniLIMS method)
fetch_export() (bbcflib.daflims.DAFLIMS method), [1], [2]
fetch_fastq() (bbcflib.daflims.DAFLIMS method), [1], [2]
fetch_file() (bein.bein.MiniLIMS.MiniLIMS method)
(bein.MiniLIMS method)
fetch_qc() (bbcflib.daflims.DAFLIMS method), [1], [2]
fields (bbcflib.track.FeatureStream attribute)
(bbcflib.track.Track attribute)
filehandle (bbcflib.track.Track attribute)
filter_scores() (in module bbcflib.gfminer.stream.scores)
flankBed() (in module bbcflib.gfminer.bedtools)
format (bbcflib.track.Track attribute)
format_float() (in module bbcflib.track)
format_int() (in module bbcflib.track)
Frontend (class in bbcflib.frontend), [1]
fusion() (in module bbcflib.gfminer.common)

G

gene_coordinates() (bbcflib.genrep.Assembly method), [1]
gene_track() (bbcflib.genrep.Assembly method), [1]
generic_merge() (in module bbcflib.gfminer.common)
genome_id (bbcflib.genrep.Assembly attribute), [1]
genomeCoverageBed() (in module bbcflib.gfminer.bedtools)
GenRep (class in bbcflib.genrep), [1]
GenrepObject (class in bbcflib.genrep)
get_bam_wig_files() (in module bbcflib.mapseq)
get_exon_mapping() (bbcflib.genrep.Assembly method), [1]
get_fastq_files() (in module bbcflib.mapseq)
get_features_from_gtf() (bbcflib.genrep.Assembly method), [1]
get_files() (in module bbcflib.common)
get_gene_mapping() (bbcflib.genrep.Assembly method), [1]
get_genrep_objects() (bbcflib.genrep.GenRep method), [1]
get_links() (bbcflib.genrep.Assembly method), [1]
get_motif_PWM() (bbcflib.genrep.GenRep method), [1]
get_primersList() (in module bbcflib.demultiplex)
get_project() (in module bbcflib.gdv)
get_range() (bbcflib.track.sql.SqlTrack method)
(bbcflib.track.text.TextTrack method)
get_sequence() (bbcflib.genrep.GenRep method), [1]
get_sqlite_url() (bbcflib.genrep.Assembly method), [1]
get_transcript_mapping() (bbcflib.genrep.Assembly method), [1]
getNearestFeature() (in module bbcflib.gfminer.stream.annotate)
getOverlap() (in module bbcflib.gfminer.bedtools)
GffTrack (class in bbcflib.track.text)
groupBy() (in module bbcflib.gfminer.bedtools)
gtf_from_bam_header() (in module bbcflib.rnaseq)
gtf_to_sql() (bbcflib.genrep.Assembly method), [1]
guess_file_format() (in module bbcflib.maplot)

H

header (bbcflib.track.text.TextTrack attribute)

I

id (bbcflib.genrep.Assembly attribute), [1]
import_file() (bein.MiniLIMS method)
index_path (bbcflib.genrep.Assembly attribute), [1]
info (bbcflib.track.Track attribute)
int_to_strand() (in module bbcflib.track)
intersect() (in module bbcflib.gfminer.stream.intervals)
intersect_many_bed() (in module bbcflib.common)
intersectBed() (in module bbcflib.gfminer.bedtools)
intersection() (in module bbcflib.gfminer.stream.intervals)
intype (bbcflib.genrep.Assembly attribute), [1]
intypes (bbcflib.track.text.TextTrack attribute)
is_up() (bbcflib.genrep.GenRep method), [1]
isnum() (in module bbcflib.common)

J

Job (class in bbcflib.frontend), [1]
job() (bbcflib.frontend.Frontend method)

L

linksBed() (in module bbcflib.gfminer.bedtools)
load_paramsFile() (in module bbcflib.demultiplex)
loadPrimers() (in module bbcflib.c4seq)

M

macs() (in module bbcflib.chipseq)
make_header() (bbcflib.track.text.TextTrack method)
map_chromosome_names() (bbcflib.genrep.Assembly method), [1]
map_chromosomes() (in module bbcflib.gfminer.common)
map_groups() (in module bbcflib.mapseq)
map_reads() (in module bbcflib.mapseq)
mapBed() (in module bbcflib.gfminer.bedtools)
MAplot() (in module bbcflib.maplot)
maskFastaFromBed() (in module bbcflib.gfminer.bedtools)
md5 (bbcflib.genrep.Assembly attribute), [1]
merge_scores() (in module bbcflib.gfminer.stream.scores)
merge_sql() (in module bbcflib.common)
mergeBed() (in module bbcflib.gfminer.bedtools)
microbiome_workflow() (in module bbcflib.microbiome)
MiniLIMS (class in bein)
motifs_available() (bbcflib.genrep.GenRep method), [1]
multiBamCov() (in module bbcflib.gfminer.bedtools)
multiIntersectBed() (in module bbcflib.gfminer.bedtools)
multiple_tracks() (in module bbcflib.gdv)

N

name (bbcflib.genrep.Assembly attribute), [1]
(bbcflib.track.Track attribute)
neighborhood() (in module bbcflib.gfminer.stream.intervals)
new_project() (in module bbcflib.gdv)
next() (bbcflib.track.FeatureStream method)
no_merge() (in module bbcflib.gfminer.common)
normalize() (in module bbcflib.gfminer.common)
(in module bbcflib.gfminer.stream.scores)
normalize_url() (in module bbcflib.common)
nr_assembly_id (bbcflib.genrep.Assembly attribute), [1]
nucBed() (in module bbcflib.gfminer.bedtools)

O

open() (bbcflib.track.text.TextTrack method)
ordered() (in module bbcflib.gfminer.common)
outtypes (bbcflib.track.text.TextTrack attribute)
overlap() (in module bbcflib.gfminer.stream.intervals)

P

pairToBed() (in module bbcflib.gfminer.bedtools)
pairToPair() (in module bbcflib.gfminer.bedtools)
parallel_bowtie() (in module bbcflib.mapseq)
parallel_density_sql() (in module bbcflib.mapseq)
parallel_density_wig() (in module bbcflib.mapseq)
parse_vcf() (in module bbcflib.snp)
parseConfig() (in module bbcflib.frontend)
path (bbcflib.track.Track attribute)
path_to_file() (bein.MiniLIMS method)
pause() (in module bbcflib.common)
(in module bein.util)
PE_fragment_size() (bbcflib.track.bin.BamTrack method)
pid (in module bein)
(ProgramOutput attribute)
plot_stats() (in module bbcflib.mapseq)
poisson_threshold() (in module bbcflib.mapseq)
pprint_bamstats() (in module bbcflib.mapseq)
prepareReport() (in module bbcflib.demultiplex)
program (class in bein)
program_exists() (in module bbcflib.common)
ProgramFailed
ProgramOutput (class in bein), [1]

R

randomBed() (in module bbcflib.gfminer.bedtools)
read() (bbcflib.track.bin.BamTrack method)
(bbcflib.track.bin.BigWigTrack method)
(bbcflib.track.sql.SqlTrack method)
(bbcflib.track.text.TextTrack method)
read_sets() (in module bbcflib.mapseq)
readonly (bbcflib.track.sql.SqlTrack attribute)
remove_duplicate_reads() (in module bbcflib.mapseq)
removeNA() (in module bbcflib.c4seq)
reorder() (in module bbcflib.gfminer.common)
require() (in module bbcflib.gfminer.stream.intervals)
resolve_alias() (bein.MiniLIMS method)
return_code (in module bein)
(ProgramOutput attribute)
RNAseq (class in bbcflib.rnaseq)
rnaseq_workflow() (in module bbcflib.rnaseq)
run() (in module bbcflib.gfminer)
run_deconv() (in module bbcflib.chipseq)
run_fastqc() (in module bbcflib.mapseq)

S

SamTrack (class in bbcflib.track.text)
score_array() (in module bbcflib.gfminer.numeric.signal)
score_by_feature() (in module bbcflib.gfminer.stream.scores)
score_threshold() (in module bbcflib.gfminer.common)
search_executions() (bein.bein.MiniLIMS.MiniLIMS method)
(bein.MiniLIMS method)
search_files() (bein.bein.MiniLIMS.MiniLIMS method)
(bein.MiniLIMS method)
segment_features() (in module bbcflib.gfminer.stream.intervals)
select() (in module bbcflib.gfminer.common)
selection() (in module bbcflib.gfminer.stream.intervals)
sentinelize() (in module bbcflib.gfminer.common)
separator (bbcflib.track.text.TextTrack attribute)
set_assembly() (bbcflib.genrep.Assembly method), [1]
set_file_descr() (in module bbcflib.common)
SgaTrack (class in bbcflib.track.text)
shuffleBed() (in module bbcflib.gfminer.bedtools)
shuffled() (in module bbcflib.gfminer.common)
single_track() (in module bbcflib.gdv)
sleep() (in module bein.util)
slopBed() (in module bbcflib.gfminer.bedtools)
snp_workflow() (in module bbcflib.snp)
sortBed() (in module bbcflib.gfminer.bedtools)
sorted_stream() (in module bbcflib.gfminer.common)
source_id (bbcflib.genrep.Assembly attribute), [1]
source_name (bbcflib.genrep.Assembly attribute), [1]
split_field() (in module bbcflib.gfminer.common)
split_file() (in module bein.util)
sqlite_path (bbcflib.genrep.Assembly attribute), [1]
SqlTrack (class in bbcflib.track.sql)
statistics() (bbcflib.genrep.Assembly method), [1]
stderr (in module bein)
(ProgramOutput attribute)
stdout (in module bein)
(ProgramOutput attribute)
strand_merge() (in module bbcflib.gfminer.common)
strand_to_int() (in module bbcflib.track)
subtractBed() (in module bbcflib.gfminer.bedtools)
summed_feature_matrix() (in module bbcflib.gfminer.numeric.regions)

T

tables (bbcflib.track.sql.SqlTrack attribute)
tagBam() (in module bbcflib.gfminer.bedtools)
task() (in module bein)
TextTrack (class in bbcflib.track.text)
timer() (in module bbcflib.common)
touch() (in module bein.util)
Track (class in bbcflib.track)
track() (in module bbcflib.track)
transcript_track() (bbcflib.genrep.Assembly method), [1]
transcriptome_gtf_from_genrep() (in module bbcflib.rnaseq)
types (bbcflib.track.sql.SqlTrack attribute)

U

ucsc_to_ensembl() (in module bbcflib.track)
union() (in module bbcflib.gfminer.stream.intervals)
unionBedGraphs() (in module bbcflib.gfminer.bedtools)
unique() (in module bbcflib.common)
unique_filename() (in module bbcflib.maplot)
unique_filename_in() (in module bbcflib.common)
(in module bein)
unroll() (in module bbcflib.gfminer.common)
untar_genome_fasta() (bbcflib.genrep.Assembly method), [1]
updated_at (bbcflib.genrep.Assembly attribute), [1]
use() (bein.Execution method)
use_pickle() (in module bein.util)

V

vec_reduce() (in module bbcflib.gfminer.numeric.signal)

W

WigTrack (class in bbcflib.track.text)
window_smoothing() (in module bbcflib.gfminer.stream.scores)
windowBed() (in module bbcflib.gfminer.bedtools)
windowMaker() (in module bbcflib.gfminer.bedtools)
write() (bbcflib.track.text.TextTrack method)
written (bbcflib.track.text.TextTrack attribute)

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