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1,000 results • Page
4 of 20
Sort: Views
Rank
Views
Votes
Replies
5
votes
5
replies
2.5k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 6 months ago by
Feng Tian
▴ 20 • written 5.6 years ago by
gewa
▴ 20
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 29 days ago by
Ram
43k • written 22 months ago by
ev97
▴ 20
2
votes
6
replies
2.4k
views
No best K value found
Assembly
Kmergenie
updated 5 months ago by
shaileshdesai76
• 0 • written 7.2 years ago by
kspata
▴ 80
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 13 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq
Somatic-Mutation
Variant-Calling
updated 7 weeks ago by
Ram
43k • written 6.2 years ago by
Sharon
▴ 610
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 28 days ago by
Ram
43k • written 4.9 years ago by
saksis.rihards
▴ 10
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV
WGS
updated 10 months ago by
Ram
43k • written 6.7 years ago by
zhang248
▴ 40
2
votes
20
replies
2.4k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
8 months ago by
Maxine
▴ 40
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 5 weeks ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
1
vote
2
replies
2.4k
views
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
vcftools
samtools
faidx
tabix
1000Genomes
updated 12 months ago by
barslmn
★ 2.1k • written 6.6 years ago by
shrutishreyajha
▴ 10
1
vote
3
replies
2.4k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 5 months ago by
ayaosama2111
▴ 10 • written 7.5 years ago by
Nicolas Rosewick
11k
1
vote
3
replies
2.4k
views
Use vcf files for dN/dS calculations
sequencing
updated 7 months ago by
rohitsatyam102
▴ 860 • written 6.4 years ago by
L. A. Liggett
▴ 120
2
votes
2
replies
2.4k
views
bcftools annotate -a
bcftools
VCF
updated 10 months ago by
Ram
43k • written 14 months ago by
anasjamshed
▴ 120
0
votes
0
replies
2.4k
views
Tool To Convert Affy Oncoscan Data Into Affy Snp6.0 Format
r
updated 11 months ago by
Ram
43k • written 10.6 years ago by
Jason
▴ 20
2
votes
5
replies
2.4k
views
GTF file for HIV strain pNL4-3
HIV
annotation
mapping
updated 10 weeks ago by
xiaoleiusc
▴ 140 • written 5.9 years ago by
caggtaagtat
★ 1.9k
1
vote
1
reply
2.3k
views
RStudio Cloud : Problem in Package Installing
RStudio
Bioconductor
updated 11 months ago by
Ram
43k • written 4.0 years ago by
Rishabh Jha
• 0
14
votes
18
replies
2.3k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 210 • written 7 months ago by
Chris
▴ 280
0
votes
0
replies
2.3k
views
Slimming or not slimming with Gene Ontology: which tool should be used?
gene-ontology
go-annotation
updated 10 months ago by
Ram
43k • written 7.8 years ago by
tlorin
▴ 360
1
vote
0
replies
2.3k
views
Inflated qq plot and genomic inflation est. lambda
gene
SNP
genome
updated 10 months ago by
Ram
43k • written 6.0 years ago by
khn
▴ 130
0
votes
1
reply
2.3k
views
Cochran-Armitage trend test
plink
updated 10 months ago by
Ram
43k • written 7.8 years ago by
toyan.j.p
▴ 30
1
vote
1
reply
2.3k
views
Tools for just generating a file including all shared variants in all VCF files
vcf
shared-variants
updated 11 months ago by
Ram
43k • written 7.8 years ago by
zengtony743
▴ 80
2
votes
5
replies
2.3k
views
Reciprocal blast commandline
Blast
updated 11 months ago by
Ram
43k • written 4.8 years ago by
baurumon
▴ 30
0
votes
11
replies
2.3k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 11 months ago by
Ram
43k • written 5.0 years ago by
saumya.sharma1509
• 0
1
vote
1
reply
2.3k
views
NS, AC, AN and AF in VCF file
VCF
updated 8 months ago by
Mwangana
• 0 • written 22 months ago by
wangdp123
▴ 340
0
votes
2
replies
2.3k
views
ROSE Algorithm for Ranking Super Enhancers
ChIP-Seq
updated 12 weeks ago by
Ram
43k • written 3.9 years ago by
mropri
▴ 150
0
votes
4
replies
2.3k
views
HOMER load genomes not working
HOMER
rna
pombe
genome
updated 11 months ago by
Ram
43k • written 3.9 years ago by
c78483
• 0
1
vote
2
replies
2.2k
views
Quantitative anlysis of alternative splicing events
RNA-Seq
updated 10 months ago by
Ram
43k • written 9.7 years ago by
Anil Kesarwani
▴ 90
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 7 months ago by
smisek
• 0 • written 3.5 years ago by
ian_chiquier
• 0
0
votes
3
replies
2.2k
views
ANGeS - Ancestral Genome reconstruction
ancestral
genome
updated 9 weeks ago by
illodukarthickbabu
• 0 • written 2.7 years ago by
alslonik
▴ 310
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein
transcript
normalisation
updated 3 months ago by
Ram
43k • written 21 months ago by
qiz218591
▴ 10
0
votes
1
reply
2.2k
views
MACS2 result analysis
peak-calling
macs2
ChIP-Seq
updated 11 months ago by
Ram
43k • written 5.0 years ago by
chaudharyc61
▴ 90
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 28 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
0
votes
1
reply
2.2k
views
monocle how to identify branches
RNA-Seq
pseudotime
monocle
updated 10 months ago by
Ram
43k • written 5.6 years ago by
hsu
▴ 40
0
votes
5
replies
2.2k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 11 months ago by
Ram
43k • written 7.8 years ago by
yoyofangliu
• 0
0
votes
3
replies
2.2k
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
11 months ago by
Mo
▴ 40
0
votes
3
replies
2.2k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 7 months ago by
aishwarya
• 0 • written 5.9 years ago by
blooming.daisy333
▴ 110
0
votes
1
reply
2.2k
views
hmmsearch didn't work with nucleotide genome
genome
hmmsearch
HMMER
updated 10 months ago by
Ram
43k • written 6.2 years ago by
lbroetto
• 0
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end
alignment
next-gen
updated 10 months ago by
Ram
43k • written 11.3 years ago by
Kenneth Daily
▴ 50
2
votes
13
replies
2.2k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 7 months ago by
Ram
43k • written 9 months ago by
epianalysis
• 0
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by
Ram
43k • written 9.1 years ago by
Harish Sanja
▴ 10
0
votes
5
replies
2.1k
views
Extra header column stopping EMMAX (C), but not seen in input files
emmax
genomics
Cpp
plink
GWAS
updated 10 months ago by
linchenshitiancai
• 0 • written 6.2 years ago by
michael.nagle
▴ 100
0
votes
2
replies
2.1k
views
Tool for manual annotation curation
annotation
updated 10 months ago by
Ram
43k • written 6.7 years ago by
Rox
★ 1.4k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
16 days ago by
anna
▴ 20
10
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
11 months ago by
yoshifumimiya
▴ 50
0
votes
2
replies
2.1k
views
How map the gene position to the genomic position.
vcf
sequence
SNP
genome
updated 10 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
0
votes
0
replies
2.1k
views
Mgrep Source Code
mgrep
updated 10 months ago by
Ram
43k • written 11.4 years ago by
Will
4.5k
0
votes
2
replies
2.1k
views
Giemsa stain annotation/nomenclature for UCSC cytoband tracks
ucsc
ggbio
gviz
hg19
updated 3 months ago by
Ram
43k • written 7.2 years ago by
maden.sean
▴ 20
0
votes
1
reply
2.1k
views
hisat2 error: Symbol not found ... libstdc++.6.dylib
hisat2
libstdc
RNA-Seq
dylib
updated 11 months ago by
Ram
43k • written 4.0 years ago by
axolootle
• 0
3
votes
6
replies
2.1k
views
Biopython TimeExceptionError how to handle?
biopython
entrez
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Xylanaser
▴ 80
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 29 days ago by
Ram
43k • written 21 months ago by
mmitra
▴ 60
1,000 results • Page
4 of 20
Recent Votes
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
Answer: Concatenate multiple paired-end reads or interleaved which is best approach to a
Scale total height phylogenetic tree
Scale total height phylogenetic tree
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Answer: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
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Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
Jeremy Leipzig
22k
We get this question like clockwork every 6 weeks. I'll say it one more time: **A freeze is a freeze.** Patches are not a thing th…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Thanks very much for your feedback! I will take all those things in consideration once I start the analysis! Just out of curiosity, do yo…
Answer: getting exon coordinates
by
ben@f
▴ 10
A combination of bash and awk can do the work, suppose you have the gff file annotation of your gene of interest and a text file with Gene…
Comment: getting exon coordinates
by
Pierre Lindenbaum
161k
https://www.biostars.org/p/385786/ ; <br> https://www.biostars.org/p/276608/ ; <br> https://www.biostars.org/p/411934/ ;etc... <!-- How …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
I would have thought `needle` from EMBOSS would be the option to use.
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 120
ok, then you should add the donor information to the PCA analysis. First create a separate dataframe for the donors, then add with `factor`…
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 180
If you are willing to do some coding I think <https://github.com/smarco/WFA2-lib> is among the fastest global aligners, the repo has C++ ex…
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
by
GenoMax
142k
There is an API that you could try: https://www.ebi.ac.uk/pride/markdownpage/prideutilities
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
by
Pierre Lindenbaum
161k
thanks. looks interesting but it's broken. the Firefox console shows a 404 for https://www.ebi.ac.uk/pride/ws/archive/v2/peptidesummary?ke…
Answer: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
by
GenoMax
142k
Perhaps: https://www.ebi.ac.uk/pride/peptidome/ This site is very slow. Almost to the point of being not usable. My search with your pepti…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
You're welcome. Yes, unfortunately you need quite a sample size for WGCNA simply because correlations with few samples are vastly underpowe…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
manuelmourato25
• 0
Ah, I see. So seen that what I want is the per-gene correlation, the minimum of 20/25 for the pearson correlation still applies. Thank you …
Answer: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
I think you're misunderstanding some concepts here. WGCNA is a framework that defines modules based on how and which genes are correlated …
Comment: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
GenoMax
142k
> most up-to-date build Major build of the genome remains GRCh38. What you are looking at is the latest patch release for that build. Only…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
manuelmourato25
• 0
Thank you @atpoint . My apologies, maybe I should rephrase the question. I read the WGCNA docs already, and for the Pearson correlation tes…
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