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103,960 results • Page
1 of 2080
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Composition-Conditioned-CrystalGAN
gans
proteinstructure
proteinfolding
pytorch
just now by
Wiktoria
• 0
0
votes
1
reply
22
views
SQL query to find all specific value in all columns based on row id.
sql
updated 26 minutes ago by
Pierre Lindenbaum
147k • written 1 hour ago by
lippithakkar
• 0
2
votes
5
replies
68
views
How to know the genome indices from STAR is correct
STAR
updated 53 minutes ago by
GenoMax
118k • written 1 hour ago by
Chris
• 0
0
votes
0
replies
15
views
Signac MACS2 peak shape question
snATAC-seq
snRNA-seq
signac
multiome
seurat
2 hours ago by
rbronste
▴ 400
0
votes
3
replies
108
views
Help with clumpify.sh
fastp
BBTools
clumpify
updated 2 hours ago by
Brian Bushnell
18k • written 12 hours ago by
tamu.anand
▴ 10
687
votes
160
replies
92k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 3 months ago by
Biostar
960 • written 5.7 years ago by
Istvan Albert
94k
2
votes
2
replies
59
views
LInear Models with HLA-B alleles in R
R
HLA
53 minutes ago by
schagas
• 0
5
votes
3
replies
62
views
How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
awk
updated 1 hour ago by
LChart
▴ 310 • written 3 hours ago by
lidan0001
▴ 50
3
votes
2
replies
56
views
How to create a fasta file using a list of DNA sequences data
linux
fasta
updated 2 hours ago by
Shred
▴ 770 • written 3 hours ago by
Alex S
▴ 20
0
votes
0
replies
27
views
D-loop in mitogenomes?
gene
genome
protein
4 hours ago by
sunnykevin97
▴ 970
0
votes
1
reply
39
views
set-all-var-ids misuse in plink 2.0
plink
rsid
updated 4 hours ago by
chrchang523
9.5k • written 5 hours ago by
hi.there
• 0
0
votes
0
replies
27
views
PennCNV-Seq
command
PennCNV-Seq
execute
the
4 hours ago by
heureuse
• 0
1
vote
1
reply
47
views
Downloading Data from ICGC via Amazon AWS EC2
ICGC
Token
updated 4 hours ago by
GenoMax
118k • written 5 hours ago by
Hashirama
▴ 20
0
votes
0
replies
28
views
ASCAT + ShallowHRD
using
status
HRD
ShallowHRD
6 hours ago by
shounak.chakraborty1990
▴ 20
0
votes
0
replies
29
views
Classify unknown TEs produced by RepeatModeler
repeats
TE
genome
6 hours ago by
kirillkirilenko.tomsk
• 0
2
votes
0
replies
32
views
Herald:
The Biostar Herald for Monday, August 08, 2022
herald
6 hours ago by
Biostar
960
5
votes
5
replies
152
views
Bam file from STAR
STAR
1 hour ago by
Chris
• 0
0
votes
1
reply
113
views
Loading the ID mapping file from Uniprot
ENSEMBL
python
UniProt
Uniprot
updated 6 hours ago by
Elisabeth Gasteiger
★ 2.1k • written 22 hours ago by
MB
• 0
0
votes
0
replies
33
views
News:
Online training - DNA methylation in plants and animals
OxfordNanopore
DNAMethylation
BSseq
longreads
PacBio
7 hours ago by
carlopecoraro2
★ 2.1k
0
votes
0
replies
39
views
Splitting Gbff files
Gbff
7 hours ago by
schlogl
▴ 110
1
vote
0
replies
61
views
Job:
Computational PostDoc positions in Tübingen Germany (medical genetics)
medical_genetics
9 hours ago by
German.M.Demidov
★ 2.8k
5
votes
3
replies
89
views
Making multiple comparison in lmFit
limma
updated 9 hours ago by
ATpoint
64k • written 9 hours ago by
krushnach80
★ 1.1k
1
vote
2
replies
147
views
Multiple Testing Correction for GO Terms
Terms
Multiple
GO
Testing
Correction
updated 4 hours ago by
Yogi
• 0 • written 22 hours ago by
Chris
▴ 10
1
vote
4
replies
135
views
How can we find disease-associated variants of a Transcript?
Variants.
Transcripts
Bioinformatics
Ensembl
Disease
8 hours ago by
Cyrille
• 0
0
votes
1
reply
75
views
phylogeny
phylogeny
genes
with
virulence
updated 9 hours ago by
Matthias Zepper
★ 1.4k • written 11 hours ago by
saifulislam99121
• 0
0
votes
1
reply
155
views
How to extract gene families for a given set of genes
gene
mus
musculus.
family
biomart
ensembl
updated 11 hours ago by
Ben_Ensembl
★ 2.0k • written 3 days ago by
noorpratap.singh
▴ 330
0
votes
0
replies
41
views
Download specific sequences from databases using a Ruby-Script
KEGG
Ruby
database
12 hours ago by
Theresa
• 0
0
votes
9
replies
196
views
filtering multi sample vcf file
vcf
filtering
file
updated 7 hours ago by
Pierre Lindenbaum
147k • written 12 hours ago by
maajid
• 0
0
votes
0
replies
38
views
facing difficulty while interpreting mean-variance trend plot in GEO2R
GEO2R
normalization
mean-variance
GEO
12 hours ago by
ElfoHelpo
• 0
0
votes
0
replies
36
views
Fetching schemes from pubMLST
Fetching
pubMLST
schemes
cgMLST
scheme
13 hours ago by
davidmaimoun
▴ 50
0
votes
1
reply
67
views
liftover bed not matching panel gene names
liftover
vcf
bed
bedtools
12 hours ago by
whb
▴ 30
0
votes
1
reply
102
views
10X genomics single cell
single
cell
updated 14 hours ago by
MohammadAlkadi
▴ 70 • written 18 hours ago by
shiviagarwalpharma
• 0
0
votes
3
replies
185
views
perl can't see path problem
protein
tool
pfamscan
updated 10 hours ago by
colindaven
★ 3.9k • written 2 days ago by
Xylanaser
▴ 80
0
votes
2
replies
176
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
normalization
batcheffect
single_cell_features
training_test_split
5 hours ago by
mmitra
▴ 40
0
votes
1
reply
121
views
STAR fails: quality string length is not equal to sequence length but only AFTER cutadapt is run
fastq
cutadapt
rna-seq
STAR
updated 9 hours ago by
ATpoint
64k • written 19 hours ago by
bioinfo_cat
• 0
0
votes
0
replies
67
views
UK Biobank vs. NIH-EBI GWAS catalogue
UK
Biobank
GWAS
NIH-EBI
20 hours ago by
Sanjar
▴ 140
0
votes
4
replies
156
views
CPTAC data download, transcriptomics
CPTAC
download
data
transcriptome
2 hours ago by
Rob
▴ 130
4
votes
3
replies
145
views
Reading in input file into a Snakemake pipeline
snakemake
updated 5 hours ago by
Shred
▴ 770 • written 1 day ago by
Timotheus
▴ 10
1
vote
1
reply
110
views
Determining strandedness of RNAseq samples from count data and understanding counts in sex genes
strandedness
htseq
RNAseq
updated 23 hours ago by
ATpoint
64k • written 1 day ago by
sr41489
• 0
0
votes
2
replies
114
views
Stringtie skips some reference genes
Stringtie
Assembly
RNA-seq
10 hours ago by
waqaskhokhar999
▴ 130
0
votes
1
reply
97
views
VCF to MAF using oncotator
vcf
maf
oncotator
to
updated 6 hours ago by
Dave Carlson
▴ 820 • written 1 day ago by
hamrejr
• 0
0
votes
0
replies
66
views
How can one identify genome segments and mutations in Influenza viruses?
Bioinformatics
influenza
viruses
1 day ago by
eennadi
▴ 20
2
votes
2
replies
142
views
Extract nucleotide sequence from a RefSeq Transcript ID
nucleotide
refseq
transcript
sequence
entrez
1 day ago by
Vincent Laufer
★ 2.2k
0
votes
2
replies
121
views
vcf2maf allele frequency not converting
tAF
AF
vcf2maf
1 day ago by
hamrejr
• 0
0
votes
0
replies
76
views
One-to-many pairwise alignment
pairwise
alignment
1 day ago by
Xiaokang
▴ 70
0
votes
0
replies
94
views
How to analyse .cdf or .mzML raw mass spectrometry files to get relative abundances of compounds in metabolome?
mass
spectrometry
data
metabolome
analysis
1 day ago by
dpc
▴ 240
0
votes
0
replies
93
views
r package for downstream analysis of phylogenetic trees
phylogenetics
R
1 day ago by
TM
• 0
0
votes
0
replies
87
views
any way to merge functions of kegg orthologs database?
functional-profile
metagenomics
data-wrangling
1 day ago by
v.berriosfarias
▴ 50
0
votes
5
replies
325
views
merging data; remove extra rows
RNA-Seq
1 day ago by
Rob
▴ 130
0
votes
0
replies
128
views
Package suggestion to calculate Protein-Protein interaction.
Free
FoldX
Binding
Affinity
Interaction
Energy
Protein-Protein
2 days ago by
UGUR
• 0
103,960 results • Page
1 of 2080
Recent Votes
Answer: Obtaining the top matches from blast
A: How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
Answer: LInear Models with HLA-B alleles in R
Comment: How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
Comment: How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
Answer: How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
Comment: How to know the genome indices from STAR is correct
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Recent Replies
Comment: SQL query to find all specific value in all columns based on row id.
by
Pierre Lindenbaum
147k
show us the schema for your database
Comment: LInear Models with HLA-B alleles in R
by
schagas
• 0
Thanks @lchart ! So would the second approach be a loss in the "accuracy" of the estimates? And Anyway, the two ways are not wrong, sinc…
Comment: Comparison between two sets of cell lines
by
Vincent
• 0
Hi indolefin, I am currently working on the same kind of question/hypothesis that you had. Did you find a tool to compare your groups of c…
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
Are you sure the genome generate job completed successfully i.e. there were no errors? Can you show a listing of the files above so we can …
Comment: How I do lift over a Plink bim file from Hg18 to Hg19.
by
pabe
▴ 10
Are you all using python2 or python3? Make sure it is python2. The liftOverPlink.py and rmBadLifts.py scripts will not work properly unless…
Comment: How to know the genome indices from STAR is correct
by
Chris
• 0
Creating genome indices took less than 1 hour with the output I listed above but the alignment is less than 1 minute so as you said there w…
Comment: How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
by
LChart
▴ 310
If your narrowPeak file has peak IDs in the NAME field you can `awk '$8 == "promoter-TSS"' x.annot | cut -f1 > peak_names.txt'` `grep -Wf…
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
Indeed. This is about "genomegenerate".
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
> Then I run alignment but the size of all output files is 0. You are not running an alignment just yet. A `STAR genomegenerate` job can t…
Comment: How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
by
lidan0001
▴ 50
The `'$8 == "promoter-TSS"'` is in the annotation file, but I want to filter the `narrowPeak` file, how can I do that? Thanks
Comment: How to know the genome indices from STAR is correct
by
Chris
• 0
I am sorry. I thought the errors are different.
Answer: Help with clumpify.sh
by
Brian Bushnell
18k
If you keep the files decompressed, there is no reason to run Clumpify unless you turn on deduplication or error-correction. However, if y…
Comment: CPTAC data download, transcriptomics
by
Rob
▴ 130
Thanks I didnot miss this but nowhere is mentioned which type of normalization was applied to the whole data file we get. it just explains …
Answer: LInear Models with HLA-B alleles in R
by
LChart
▴ 310
Your first approach can be visualized as this picture: ![Multi-linear regression][1] With the "(Intercept)" coefficient, in your case, c…
Comment: CPTAC data download, transcriptomics
by
GenoMax
118k
Did you miss this: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#mrna-expression-transformation
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