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50 results • Page
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Showing top results for tag:
ensembl
•
reset
1
vote
3
replies
81
views
X amino acid in ensembl
aminoacid
alignment
ensembl
protein
sequence
updated 5 hours ago by
Mensur Dlakic
★ 10k • written 9 hours ago by
Jason
• 0
4
votes
4
replies
89
views
Which Fasta file and GTF file to use in STAR alignment
STAR
ENSEMBL
GTF
fa
12 hours ago by
peru
• 0
1
vote
2
replies
165
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl
VEP
VCF
updated 3 days ago by
ATpoint
48k • written 5 days ago by
dare_devil
★ 1.4k
5
votes
3
replies
197
views
Unable to match Ensembl IDs from TCGA-related CNV datasets
Ensembl
Number
TCGA
TCGABiolinks
Variation
Copy
updated 9 days ago by
Kevin Blighe
72k • written 13 days ago by
dc37
▴ 20
10
votes
8
replies
557
views
ENSMUSG number convert to gene name
ensembl
gene
updated 20 days ago by
Kevin Blighe
72k • written 22 days ago by
yueli7
▴ 210
3
votes
4
replies
307
views
How do we handle TPM values after converting from Ensembl to HUGO genes?
ensembl
hugo
tpm-calculator
tpm
rna-seq
updated 23 days ago by
Istvan Albert
87k • written 23 days ago by
Jordan
★ 1.2k
0
votes
0
replies
87
views
ENSEMBL bigwig RNA-seq tracks for single-gene visual inspection
RNA-Seq
tracks
bigwig
ensembl
zebrafish
25 days ago by
bernarda
• 0
3
votes
3
replies
3.1k
views
Playing With Mysql/Ensembl (I): Mapping 'Gene' To 'Xref'
ensembl
mysql
updated 28 days ago by
Biostar
20 • written 11.0 years ago by
Pierre Lindenbaum
135k
0
votes
3
replies
149
views
Read VEP output from command line in R
vep
ensembl
R
Bash
updated 29 days ago by
prasundutta87
▴ 470 • written 29 days ago by
yussab
▴ 30
0
votes
2
replies
109
views
Is the ENSEMBL FTP down?
ensembl
ftp
29 days ago by
liorglic
▴ 340
92
votes
12
replies
38k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl
entrez
gene
updated 4 weeks ago by
hagenaue
• 0 • written 9.2 years ago by
Untom
▴ 390
5
votes
8
replies
419
views
Question: Convert Ensembl Transcript Ids Ensmust To Gene Symbol In R
R
ENSEMBL
gene
updated 11 days ago by
Kevin Blighe
72k • written 4 weeks ago by
sugus
▴ 60
1
vote
3
replies
156
views
How to extract the longest CDS from Homo_sapiens.GRCh38.cds.all.fa?
python script
biopython
ensembl
5 weeks ago by
omotosoolatunde01
• 0
2
votes
1
reply
145
views
Ensembl REST to download transcript fastas
ensembl
updated 5 weeks ago by
Emily_Ensembl
22k • written 6 weeks ago by
H Miller
• 0
0
votes
1
reply
145
views
Virtual Box of VEP tool for windows
vep
virtualbox
ensembl
Tool
updated 6 weeks ago by
cpad0112
15k • written 6 weeks ago by
shwetan
• 0
2
votes
0
replies
117
views
News:
Free Ensembl Browser and REST API virtual workshops in March
Ensembl
training
REST API
workshop
genome browser
News
updated 6 weeks ago by
GenoMax
99k • written 6 weeks ago by
Michal @Ensembl
▴ 90
0
votes
1
reply
92
views
How do I add a GENSCAN track to the Ensembl Gene Summary
Ensembl
genscan
updated 6 weeks ago by
Emily_Ensembl
22k • written 6 weeks ago by
melissachua90
• 0
0
votes
1
reply
99
views
Incomplete MGI to ensembl conversion using Bioc version 3.12
bioMart
Ensembl
gene conversion
R
6 weeks ago by
Adriano.Biasini
• 0
1
vote
8
replies
662
views
Multiple ensembl gene ID for the same gene name (Symbol), how to deal with this while differential analysis?
RNA-Seq
alignment
next-gen
ensembl
7 weeks ago by
Swarna
• 0
3
votes
3
replies
3.8k
views
Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Sequence
RNA-Seq
SNP
genome
Mappping
ENSEMBL
updated 7 weeks ago by
Biostar
20 • written 4.2 years ago by
inambioinfo
▴ 110
1
vote
1
reply
147
views
Splice junction coordinates for Ensembl transcripts
Ensembl
Splicing
Annotation
updated 7 weeks ago by
Emily_Ensembl
22k • written 7 weeks ago by
AJ_S
• 0
3
votes
7
replies
156
views
Trying to refine REST API query
R
ensembl
API
updated 8 weeks ago by
Emily_Ensembl
22k • written 8 weeks ago by
aroso491
• 0
3
votes
4
replies
167
views
diferentially expressed ensembl ID to gene symbol conversion
DEG
Ensembl
HGNC_symbol
biomart
8 weeks ago by
imaparna27
• 0
0
votes
5
replies
160
views
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
ensembl
mapping
homology
9 weeks ago by
nickhir
▴ 30
1
vote
7
replies
186
views
Extract longest transcript from Ensembl gene table
bash
gene
ensembl
R
9 weeks ago by
Midge
• 0
6
votes
6
replies
289
views
probe ID to ensemble
conversion
ensembl
probe id
9 weeks ago by
dxodnd
• 0
4
votes
4
replies
194
views
WTF with the ensembl human genome?
genome
ensembl
refseq
updated 10 weeks ago by
Emily_Ensembl
22k • written 10 weeks ago by
Juke34
★ 5.3k
5
votes
5
replies
221
views
Why VEP doesn't take strand into account?
vep
ensembl
snp
updated 10 weeks ago by
Emily_Ensembl
22k • written 10 weeks ago by
magnolia
• 0
3
votes
7
replies
190
views
Why VEP annotates non-variants (homozygous reference)?
vep
ensembl
SNP
updated 10 weeks ago by
Emily_Ensembl
22k • written 10 weeks ago by
magnolia
• 0
0
votes
3
replies
176
views
VEP cache issues
software error
ensembl
vep
updated 11 weeks ago by
Emily_Ensembl
22k • written 11 weeks ago by
storm1907
• 0
2
votes
8
replies
222
views
Understanding Variant Effect Predictor results
ensembl
vep
variant effect predictor
11 weeks ago by
caro-ca
▴ 20
0
votes
6
replies
234
views
Unable to find this E coli genome
E coli
genome
ensembl
bacteria
download
updated 3 months ago by
Mensur Dlakic
★ 10k • written 3 months ago by
pomodoro_sinensis
• 0
6
votes
5
replies
174
views
Is there a package that outputs gene coordinates given a list of Ensembl IDs?
ensembl
biopython
gene
updated 3 months ago by
ATpoint
48k • written 3 months ago by
dustyl259
• 0
2
votes
3
replies
208
views
Does VEP use alternative splicing in their calculations?
VEP
Ensembl
Variant Effect Predictor
updated 3 months ago by
Emily_Ensembl
22k • written 3 months ago by
caro-ca
▴ 20
3
votes
4
replies
199
views
mapping gene type or biotype to ENSEMBL ID
Annotation
ensembl
Org.Hs.eg.db
biomaRt
updated 3 months ago by
rpolicastro
5.1k • written 3 months ago by
basuanubhav
▴ 10
198
votes
30
replies
112k
views
22 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 3 months ago by
zlbio12
• 0 • written 8.1 years ago by
Malachi Griffith
18k
0
votes
1
reply
174
views
Searching a DNA sequence for eukaryotic genes
fasta
ensembl
dna
human chromosome 13
updated 3 months ago by
GenoMax
99k • written 3 months ago by
mohammad.shoumik.saad.aarman
• 0
2
votes
2
replies
307
views
How to how "Gene Legend", "Regulation Legend" & "Human cDNAs" for a DNA sequence
ensembl
3 months ago by
mohammad.shoumik.saad.aarman
• 0
12
votes
11
replies
2.5k
views
How to deal with the case that one gene symbol matches multiple ensembl ids?
RNA-Seq
ensembl
updated 4 months ago by
Biostar
20 • written 2.4 years ago by
dz2353
▴ 110
3
votes
3
replies
306
views
Is there any tool/API available to convert GTF/GFF to JSON format?
gtf
gff
json
ncbi
ensembl
updated 4 months ago by
vkkodali
★ 2.5k • written 4 months ago by
lakhujanivijay
5.4k
41
votes
6
replies
9.6k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf
vcf
ensembl
tcga
somatic
Tutorial
4 months ago by
Cyriac Kandoth
5.5k
0
votes
3
replies
202
views
How to convert E. coli gene names from biocyc to Ensembl IDs?
ENSEMBL
biocyc
Escherichia coli
conversion
R
updated 4 months ago by
Biostar
20 • written 4 months ago by
Macspider
★ 3.4k
1
vote
1
reply
213
views
Problem with BiomaRt::useMart function Landscape Genomics
landcape genomics
BiomaRt
usaMart
ensembl
plant
updated 4 months ago by
Emily_Ensembl
22k • written 4 months ago by
simone.castellana
▴ 10
2
votes
4
replies
297
views
Retrieve 5'UTR sequences for ensembl_transcript_id's with unique start/end positions
biomart
ensembl
R
sequence
4 months ago by
omit3333
• 0
1
vote
1
reply
161
views
How to find the gene name and classification using Ensembl ID?
genome
ensembl
lncRNA
updated 5 months ago by
Jean-Karim Heriche
24k • written 5 months ago by
mathavanbioinfo
▴ 60
0
votes
0
replies
183
views
How do I get a gtf file to use rnaQUAST
rnaQUAST
ensembl
gencode
gtf
gff
5 months ago by
kristina.mahan
▴ 130
1
vote
4
replies
239
views
How to get enome feature annotation through NCBI api ?
refseq
NCBI
ensembl
ucsc
gene
updated 5 months ago by
Carambakaracho
★ 2.4k • written 5 months ago by
demolidd77
▴ 40
3
votes
7
replies
425
views
biomaRt error while converting ensembl gene Id to uniprot ID
biomaRt
R
ensembl
uniprot
5 months ago by
manaswwm
▴ 130
8
votes
2
replies
723
views
What is the VEP Impact column?
VEP
sequencing
consequence
variant
ensembl
written 5 months ago by
nub6
▴ 20
2
votes
0
replies
228
views
News:
Get Ensembl training, virtually
ensembl
training
online
News
5 months ago by
Emily_Ensembl
22k
50 results • Page
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Answer: Hunting invisible characters?
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Thank you, using `dos2unix` worked perfectly!
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I think the numbers you cite are the most extreme values that people will still accept. In most cases I would go for lower p-values (at lea…
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