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mandricigor
/
imrep
ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
https://mandricigor.github.io/imrep/
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Installation issues
#46
justalilibit
opened
5 months ago
0
Can not use dockers: can't open file 'setup.py': [Errno 2] No such file or directory.
#45
JianGuoZhou3
opened
2 years ago
0
Missing license
#44
DzmitryGB
opened
3 years ago
1
Provide Docker File for ImReP
#43
jkbenotmane
closed
3 years ago
1
ImRep complaining about index file being older than the BAM file
#42
vihaj
opened
3 years ago
2
question about using unmapped reads from Hisat2
#41
dingxm
opened
3 years ago
0
extract_mapped() function takes 3 arguments when specifying --digGold
#40
alexpan82
opened
4 years ago
0
Problem with installation
#39
tAndreani
closed
4 years ago
4
modify to make it compatible with clonality.py
#38
dormeight
opened
4 years ago
0
bugs of compare.repertories.py
#37
dormeight
opened
4 years ago
1
options
#36
smangul1
opened
5 years ago
0
Old suffix_tree dependance
#35
sergiigladchuk
opened
5 years ago
0
PCLfile error in eADAGE
#34
nsrilaxmi
closed
6 years ago
0
Does imrep work with BAM files from HISAT2 aligner?
#33
ooondrej
closed
6 years ago
3
unmapped reads in fastq/fasta format and pair-end data
#32
YiweiNiu
opened
6 years ago
4
run second step only for 50 bp reads
#31
smangul1
closed
6 years ago
0
-f doesn't work as expected
#30
smangul1
opened
6 years ago
0
fix clonality.py - extracting J instead of V
#29
smangul1
closed
6 years ago
1
Change the format to be , delimited
#28
smangul1
opened
6 years ago
0
errors associated to pysam
#27
oeco28
closed
6 years ago
3
further improvements
#26
smangul1
opened
7 years ago
0
something is wrong with VDJ recombinations
#25
mandricigor
closed
7 years ago
0
added --noCast option
#24
mandricigor
closed
7 years ago
0
typo in header
#23
smangul1
closed
7 years ago
1
please report in the default mode
#22
smangul1
opened
7 years ago
0
DNA seq of CDR3
#21
smangul1
opened
7 years ago
2
bug
#20
smangul1
opened
7 years ago
2
incorrect read names in partial_cdr3.txt
#19
smangul1
closed
7 years ago
2
add instalation script
#18
smangul1
closed
7 years ago
0
W in TRB
#17
smangul1
closed
7 years ago
1
save partialcdr3 at the same dir where full cdr3 are saved
#16
smangul1
closed
7 years ago
1
Total number of reads mapped to CDR3
#15
smangul1
closed
7 years ago
3
TRG
#14
smangul1
closed
7 years ago
5
ASAP!
#13
smangul1
closed
7 years ago
1
partial_cdr3.txt
#12
smangul1
closed
7 years ago
1
Output CDR3 nucleotide sequence
#11
PoslavskySV
closed
7 years ago
1
Input files for ImRep
#10
PoslavskySV
closed
7 years ago
1
output by chan
#9
smangul1
closed
7 years ago
1
fastq
#8
smangul1
closed
7 years ago
2
include header for full_cdr3.txt in the file as the first line
#7
smangul1
closed
7 years ago
1
read names have extra /1
#6
smangul1
closed
7 years ago
1
filter CDR3 with stop codon
#5
smangul1
closed
7 years ago
1
full_cdr3.txt
#4
smangul1
closed
7 years ago
5
additional output
#3
smangul1
closed
7 years ago
2
bug in output
#2
smangul1
closed
7 years ago
1
flag
#1
smangul1
closed
7 years ago
1