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mhammell-laboratory
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TEtranscripts
A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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how to extract the TE abundance
#44
xiaocong3333
closed
4 years ago
5
TEcounts Zero Values Not Chr in GTF Error
#43
mmilevskiy
closed
4 years ago
7
Difference between provided GTF files and the one downloaded from UCSC
#42
MengjunWu
closed
4 years ago
2
TE transcript output
#41
SalimMegat
closed
5 years ago
7
DESeq Normalization Questions
#40
jimcdonald
closed
5 years ago
6
Using TCGA bam files
#39
ge2sasag
closed
5 years ago
1
Problem with installation
#38
olferievm
closed
5 years ago
3
DESeq error
#37
CodyS5
closed
5 years ago
2
No comments in TE.gtf allowed
#36
foriin
closed
5 years ago
4
Error while reading bam files
#35
SalimMegat
closed
5 years ago
4
TEtranscripts and covariates values
#34
vasilislenis
closed
5 years ago
9
TE gff3 to gtf?
#33
oronoc1210
closed
5 years ago
58
Documentation for reformatting TE GTF file
#32
AlicePsyche
closed
5 years ago
7
Stranded libraries
#31
retrogenomics
closed
5 years ago
5
TEcount vs TEtranscripts
#30
retrogenomics
closed
5 years ago
3
Possible README issue with outAnchorMultimapNmax
#29
davidecarlson
closed
5 years ago
2
library requirement for tetoolkit
#28
zy041225
closed
6 years ago
2
S. cerevisiae TE annotation file
#27
lfra
closed
6 years ago
2
Bioconda package
#26
bgruening
closed
5 years ago
2
Zero TE counts
#25
lfra
closed
6 years ago
3
Treatment vs control and DeSeq2 alternative
#24
GiuliaPasquesi
closed
5 years ago
6
FTP APGv4 TE GTF - Missing semi-colon in attributes field
#23
PriceJon
closed
6 years ago
2
Lots of unannotated reads
#22
MonkeySylvia
closed
6 years ago
4
Personal GTF file
#21
MonkeySylvia
closed
6 years ago
10
results format based on "transcript_id"
#20
vasilislenis
closed
6 years ago
3
Input/output error
#19
gmachaj
closed
6 years ago
4
Deal with samples in multiple stages
#18
xinl22
closed
6 years ago
6
multi-threading
#17
retrogenomics
closed
6 years ago
16
Question about the alignments preparation
#16
vasilislenis
closed
6 years ago
6
How long to build TE index from hg19_rmsk_TE.gtf?
#15
dtsgx
closed
6 years ago
6
Where can I download the GTF file for hg38?
#14
insidemymind
closed
7 years ago
3
Whether TEtranscripts can calculate TE expression level of transcripts (NOT Gene)?
#13
xflicsu
closed
5 years ago
3
TE.gtf fails to generate index --> no TE diff expression output
#12
bdweave
closed
6 years ago
3
Problem with samtools
#11
rtmag
closed
6 years ago
18
tetranscripts incompatible with pysam >= 0.9.0
#10
rvalieris
closed
6 years ago
2
Support pysam>=0.9 and samtools>=1.3
#9
ntkme
closed
7 years ago
0
Comment and Formatting Cleanup Feature Request.
#8
molikd
closed
4 years ago
0
Create TEGroomer Functionality
#7
molikd
closed
4 years ago
2
Error when using personal TE GTF file
#6
casimonet
closed
7 years ago
9
TEcount
#5
dpryan79
closed
6 years ago
10
Can not run TEtranscripts with test files.
#4
jdaron
closed
8 years ago
2
workout long term fix for README problem
#3
molikd
closed
9 years ago
1
Edit readme to include recomendation paragraphs
#2
molikd
closed
9 years ago
1
Remove 'R' Dependency ( and therefore DESeq )
#1
molikd
closed
1 year ago
7
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