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t-neumann
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slamdunk
Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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O
#162
tianwwwwww
closed
2 weeks ago
0
alleyoop uttrates error
#161
mmaslon
opened
1 month ago
11
slamdunk all: No tcount files and no error
#160
andtsouris
opened
1 month ago
3
Application to Amplicon-Seq Libraries
#159
Rinyaveion
opened
2 months ago
1
samplesheet
#158
mmaslon
closed
3 months ago
4
/count folder empty
#157
Magisterh1
closed
4 months ago
1
Add cB file information to documentation
#156
isaacvock
opened
4 months ago
0
Implement mixture model compatibility in full pipeline
#155
isaacvock
opened
5 months ago
16
Implement mixture model compatibility
#154
isaacvock
closed
5 months ago
5
Proposal for a new Alleyoop: convenient summary of `dump` output
#153
isaacvock
opened
5 months ago
1
about 3utr numbers
#152
bioinformatica
closed
5 months ago
4
Update stats.py
#151
BRYZAL
closed
5 months ago
0
My slam-seq sequencing data only has 60-70% reads mapped to the genome
#150
bioinformatica
closed
5 months ago
4
stranded library alignment
#149
ZiggeyQi
closed
5 months ago
8
4SU labeled mRNA library built using the total RNAseq
#148
bioinformatica
opened
5 months ago
7
about pair-end data
#147
bioinformatica
closed
5 months ago
1
About calculating T>C reads CPM
#146
bioinformatica
closed
5 months ago
10
IndexError: list index out of range errror when running alleyoop tcperreadpos
#145
BRYZAV
closed
5 months ago
9
So many T2C conversion in no-4sU treated control samples
#144
realzhang
closed
5 months ago
3
strand-specific SLAM-seq analysis
#143
ZiggeyQi
closed
7 months ago
8
alleyoop dedup, samtools failed to create index because reads are not sorted
#142
algaebrown
closed
7 months ago
2
Please help me to understand why we need alleyoop collapse.
#141
realzhang
closed
5 months ago
3
mapping skipped sorting and indexing
#140
Error-fre
closed
5 months ago
12
Please help me understand the output format of alleyoop dump.
#139
realzhang
closed
8 months ago
4
mRNA half life calculation
#138
ZoeyYang912
closed
8 months ago
11
Errors with Slamdunk Count / Alleyoop Utrrates
#137
zaroogz
closed
8 months ago
25
KeyError: "tag 'XI' not present". what does identity value mean?
#136
zhouyjjj
opened
11 months ago
4
RuntimeError("Error while executing command: \"" + cmd + "\"")
#135
aishwarya-gondane
closed
5 months ago
5
Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).
#134
Umair1441
opened
1 year ago
15
Try to run Slamdunk but failed
#133
Umair1441
closed
1 year ago
13
Regions with overlapping 3'UTRs annotated
#132
os306
closed
8 months ago
6
Issue installing slamdunk
#131
airiskic
closed
1 year ago
1
UTR regions
#130
ChristianRohde
closed
1 year ago
1
Trimmed reads caused slamdunk to stop at count
#129
tiffge
closed
1 year ago
3
Effect of --slam-seq 2 parameter in NextGenMap call?
#128
isaacvock
closed
1 year ago
2
How to interpret the bigwig values?
#127
gdolsten
closed
8 months ago
3
DESeq2 for SLAM-seq
#126
gdolsten
opened
1 year ago
7
map function fails part way through samples
#125
tiffge
closed
1 year ago
18
Dockerfile bugged
#124
mattheatley
opened
1 year ago
1
Downstream analysis
#123
paulinarosales
closed
1 year ago
1
Genomic locations of the TC reads
#122
aishwarya-gondane
closed
1 year ago
3
3'UTR length
#121
Choopanian-Peyman
opened
1 year ago
4
Are alleyoop rates and multiqc plots snp corrected?
#120
seb-mueller
closed
5 months ago
3
Correlation half-life calculation and DESeq2?
#119
quarkaffi
closed
1 year ago
7
Use slamdunk -all get the filter dicrectory "_mapped_filtered.bam " file just 8kb?
#118
lillianj97
closed
5 months ago
31
slamdunk snp(varscan2) missing SNP around INDEL
#117
dyinboisry4u
closed
5 months ago
9
RuntimeError while executing command slamdunk map
#116
cz0430
closed
5 months ago
2
Question about "-e" parameter
#115
bocheng97
closed
5 months ago
1
"More columns than column names" error message when running alleyoop utrrates
#114
cz0430
closed
5 months ago
7
ReadCount to get number of reads mapped?
#113
my-linh-luu
closed
5 months ago
2
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