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41 results • Page
1 of 1
Sort: Votes
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64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 18 hours ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
8
votes
10
replies
3.2k
views
8 follow
Venter Genome Vcf
vcf
updated 15 hours ago by
Jeremy Leipzig
22k • written 10.1 years ago by
win
▴ 980
5
votes
9
replies
3.2k
views
Delete some INFO header lines and columns data
vcf
bash
vcftools
updated 9 hours ago by
tomas4482
▴ 400 • written 2.3 years ago by
pablo.goiko
• 0
4
votes
2
replies
245
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
salmon
updated 9 hours ago by
Ram
44k • written 3 days ago by
Tonya S.
▴ 10
3
votes
2
replies
200
views
vg autoindex seems stuck after a week of running
vg
pangenome
4 hours ago by
StevieP
▴ 10
3
votes
10
replies
5.3k
views
6 follow
txt file to bigwig
MEME
bigwig
updated 14 hours ago by
ATpoint
82k • written 8.6 years ago by
tanni93
▴ 50
3
votes
2
replies
138
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 2 hours ago by
zx8754
11k • written 22 hours ago by
Assa Yeroslaviz
★ 1.9k
3
votes
3
replies
835
views
Cut&Run and heatmap
and
bowtie2
MACS2
updated 16 hours ago by
sogand
• 0 • written 13 months ago by
qudrat.nii
▴ 10
2
votes
2
replies
181
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 2 hours ago by
zx8754
11k • written 21 hours ago by
vmpsb
• 0
2
votes
6
replies
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 20 hours ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
Shred
★ 1.4k
2
votes
4
replies
1.1k
views
samtools mpileup error - 1 samples in 1 input files
samtools
BAM
mpileup
SAM
updated 17 hours ago by
Damla
• 0 • written 2.4 years ago by
joseph.kelly.94
▴ 10
2
votes
4
replies
361
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
16 hours ago by
Pegasus
▴ 100
2
votes
2
replies
177
views
Search within posts based on tags using the Biostars API
api
meta
6 hours ago by
Bálint
▴ 10
2
votes
7
replies
1.6k
views
Problems when trying to use ensembl-vep
ensembl
ensembl-vep
docker
updated 4 hours ago by
tomas4482
▴ 400 • written 10 months ago by
langziv
▴ 50
2
votes
7
replies
370
views
Z score
Z-score
updated 2 hours ago by
ATpoint
82k • written 5 days ago by
Akash D
▴ 60
1
vote
2
replies
155
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
4 hours ago by
Mohamed Abderrahmane
▴ 20
1
vote
0
replies
42
views
Is there any minimum number of counts in scRNAseq to consider that a gene is expressed?
scRNAseq
single-cell
seurat
scanpy
UMI
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
ev97
▴ 20
1
vote
5
replies
151
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 1 hour ago by
SamGG
▴ 20 • written 13 hours ago by
vmpsb
• 0
1
vote
3
replies
289
views
Failed to download data from EBI with ascp
EBI
aspera
updated 4 hours ago by
jude
• 0 • written 6 weeks ago by
biock
▴ 60
0
votes
0
replies
111
views
News:
Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
Genotype-Likelihoods
Low-Coverage
Population-Genomics
ANGSD
updated 9 hours ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
37
views
EXOME DEPTH - CNV
CNV
5 hours ago by
Neha
• 0
0
votes
2
replies
306
views
Annotating single cell data automatically
single-cell
updated 4 hours ago by
Nat.Nataren
▴ 10 • written 5 weeks ago by
Gerard
• 0
0
votes
2
replies
69
views
dbNSFP4.7a database format to Annovar Format?
annotation
snp
dbNSFP
NGS
annovar
updated 4 hours ago by
Pierre Lindenbaum
162k • written 5 hours ago by
Clark_BioMorgan
▴ 50
0
votes
6
replies
500
views
How to build ribosomal interval files to use in CollectRnaSeqMetrics for hg38.p14
hg38.p14
ribosomal-intervals
10 minutes ago by
naaj
• 0
0
votes
0
replies
98
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
18 hours ago by
Ghada
• 0
0
votes
1
reply
62
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
updated 2 hours ago by
zx8754
11k • written 4 hours ago by
ashaneev07
▴ 20
0
votes
0
replies
22
views
Regarding ENSEMBL/Gencode and UCSC differences (ATAC-seq, ChiPseeker peaks annotation)
ATAC-seq
CHiPseeker
Annotation
2 hours ago by
Manko47
• 0
0
votes
1
reply
205
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
updated 23 hours ago by
raphael.B
▴ 520 • written 3 days ago by
irebekah.c
• 0
0
votes
3
replies
265
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 22 hours ago by
ATpoint
82k • written 2 days ago by
Sara
▴ 30
0
votes
1
reply
53
views
coding and non-coding region of the viral genome
region
non-coding
coding
viral
genome
updated 2 hours ago by
dthorbur
★ 2.0k • written 5 hours ago by
Ghada
• 0
0
votes
2
replies
203
views
How to decrease the motif score?
scores
Motif
updated 2 hours ago by
dthorbur
★ 2.0k • written 2 days ago by
Hadia
• 0
0
votes
2
replies
89
views
Salmon ~ Effective Length
Salmon
updated just now by
GenoMax
142k • written 9 hours ago by
chrisk
• 0
0
votes
0
replies
17
views
Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
1 hour ago by
Ian
6.0k
0
votes
1
reply
141
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
updated 1 hour ago by
dthorbur
★ 2.0k • written 4 days ago by
Emily
▴ 20
0
votes
0
replies
50
views
Calculating F_IS, F_IT on ancient DNA
adna
13 hours ago by
devenvyas
▴ 740
0
votes
0
replies
51
views
The number of region with the motif sequence is different between HOMER outputs
findMotifsGenome
HOMER
annotatePeaks
13 hours ago by
Aki
▴ 20
0
votes
2
replies
115
views
identify the coordinate for coding and non_coding region.
coding
non_coding
18 hours ago by
Ghada
• 0
0
votes
0
replies
47
views
Funcotator gnomAD incoherent number of output fields
gatk
fields
gnomAD
Funcotator
9 hours ago by
jaime alvarez
▴ 30
0
votes
1
reply
106
views
Help with proteomics downstream analysis
mass-spectrometry
proteomics
updated 9 hours ago by
Ram
44k • written 19 hours ago by
Álvaro
• 0
0
votes
0
replies
48
views
How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Package?
multi-omics
CNV
R
updated 9 hours ago by
Ram
44k • written 11 hours ago by
Ngrin
• 0
0
votes
0
replies
93
views
Determining rs ids from SNP HGV base ID?
rsID
HGV
SNP
updated 9 hours ago by
Ram
44k • written 1 day ago by
Katherine
• 0
41 results • Page
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Recent Votes
Answer: Getting the protein Domain architecture from a domtblout
Answer: Getting the protein Domain architecture from a domtblout
Multiple testing correction in RNA-Seq
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
Answer: Help me with Heatmap
Answer: Trouble understanding seemingly contradicting results of GSE analysis (contradic
Comment: Error with Pheatmap ()
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Comment: How to build ribosomal interval files to use in CollectRnaSeqMetrics for hg38.p
by
naaj
• 0
How to make sure the larger rRNAs are included?
Comment: Error with pheatmap - 'from' must be a finite number
by
SamGG
▴ 20
Please report ``` all(is.finite(mat.z)) all(is.finite(dist(mat.z))) pheatmap(mat.z, cluster_rows = FALSE, cluster_cols = FALSE) pheatmap(ma…
Comment: finding highly divergent orthologs using exonerate
by
dthorbur
★ 2.0k
It might be worth trying to cluster sequences with a few intermediate species too. Then the centroid of the cluster can theoretically be on…
Comment: Error with pheatmap - 'from' must be a finite number
by
vmpsb
• 0
> any(is.infinite(mat.z)) [1] FALSE
Comment: Error with pheatmap - 'from' must be a finite number
by
vmpsb
• 0
Thanks, how should I proceed?
Comment: Z score
by
ATpoint
82k
Difference is that plotting Z-scores plots each group and logFC plots differences between groups. Simply a different way of showing things.…
Comment: How to decrease the motif score?
by
dthorbur
★ 2.0k
You seem to indicate you found motifs. So why do you now want to reduce the score? Do you want to narrow your search to fewer motifs to mov…
Comment: coding and non-coding region of the viral genome
by
dthorbur
★ 2.0k
Are there already annotations published for the genome? If so, I doubt there is a dedicated tool since this is a simple task of parsing the…
Answer: Error with Pheatmap ()
by
zx8754
11k
Errors and warnings are clear, we can reproduce them with this simple example Somewhere *pheatmap* is getting a minimum value excluding NA…
Comment: Polygenic Risk Score calculation
by
zx8754
11k
A single PRS number is meaningless without background data like 1000 genomes, UK Biobank, etc.
Comment: Salmon vs Kallisto vs RSEM
by
Mohamed Abderrahmane
▴ 20
Thank you so much for your response. The two links are really helpful. I appreciate it. Have a nice day!
Comment: vg autoindex seems stuck after a week of running
by
StevieP
▴ 10
Thanks for this. As a follow-up, the process did indeed complete after 8.5 days so I guess my concerns were unwarranted in the end.
Comment: Problems when trying to use ensembl-vep
by
tomas4482
▴ 400
I won't recommend using conda for installation. The environment is somehow very difficult to set up. Conda will always fail to recognize so…
Comment: Failed to download data from EBI with ascp
by
jude
• 0
I'm also facing the same error
Comment: dbNSFP4.7a database format to Annovar Format?
by
Pierre Lindenbaum
162k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
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