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122,008 results • Page
611 of 2441
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1
vote
1
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1.3k
views
How can the output be renamed when converting genbank files into GFF3 format with BioPerl?
gff3
bioperl
rna-seq
genbank
genbank2gff3.pl
4.2 years ago by
Constanza
• 0
3
votes
6
replies
1.9k
views
Strand specific library
htseq
updated 4.2 years ago by
benformatics
4.2k • written 4.2 years ago by
esimonova.me
▴ 30
9
votes
4
replies
6.2k
views
Can I perform scRNAseq data integration without loosing features?
scRNAseq
anchor
integration
Seurat
features
4.2 years ago by
joker33
▴ 150
0
votes
0
replies
1.9k
views
How to create an upset plot with a count of genes per pathway in cluster-profiler?
enrichment
R
dose
plot
gene
upset
4.2 years ago by
DN99
▴ 20
2
votes
2
replies
1.9k
views
DESeq2 results difference using contrast and single conditions
DESeq2
RNAseq
4.2 years ago by
User000
▴ 750
4
votes
6
replies
4.0k
views
interaction energy using foldx to calculate stability
chains
foldx
protein
stability
4.2 years ago by
sba5k
• 0
0
votes
0
replies
1.1k
views
Multiple tests between multiple conditions and covariates with sleuth
kallisto
R
sleuth
4.2 years ago by
danjs116
• 0
0
votes
6
replies
2.1k
views
Can it be useful to depict variable genes using non-log transformed counts?
variance
rnaseq
heatmap
updated 4.0 years ago by
ATpoint
89k • written 4.3 years ago by
N15
▴ 160
2
votes
5
replies
1.7k
views
opening downloaded files from STRING protein network without R
protein
STRING
network
updated 2.6 years ago by
Ram
45k • written 4.2 years ago by
fionajcunningham
• 0
0
votes
4
replies
1.6k
views
Quantify transcriptomic shift between two conditions for each cluster
scRNAseq
seurat
singlecell
RNAseq
3.2 years ago by
Wocher33
▴ 10
3
votes
5
replies
1.7k
views
False positive adaptor findings on FastQC/MultiQC using BBMaps randomreads.sh
FastQC
adaptors
BBMap
simulated
reads
updated 4.2 years ago by
GenoMax
154k • written 4.2 years ago by
GLR
▴ 20
1
vote
3
replies
1.8k
views
Guided bioinformatics Python projects
python
learning
updated 4.1 years ago by
Ram
45k • written 4.2 years ago by
mmarcell
• 0
0
votes
0
replies
706
views
SKAT burden analysis in R
association
analysis
variant
skat
rare
4.2 years ago by
afergused
• 0
0
votes
0
replies
663
views
Annotating variants from a sequence and list of position-specific variants
variant-effect-predictor
variant-annotation
vep
4.2 years ago by
manaswwm
▴ 570
1
vote
3
replies
1.1k
views
Finding homologs in BLASTN
genomics
comparative
updated 4.2 years ago by
GenoMax
154k • written 4.2 years ago by
Meeeee
• 0
1
vote
2
replies
1.2k
views
Mapsplice2
Mapsplice2
updated 4.2 years ago by
Ram
45k • written 4.2 years ago by
nkmalini97
• 0
1
vote
4
replies
4.0k
views
RNAseq - GBFF cannot be converted to GTF
Genome
GBFF
GTF
NCBI
RNAseq
4.2 years ago by
sacdefruits
• 0
0
votes
0
replies
845
views
Caffeinate alternative for Docker
Docker
Caffeinate
updated 2.9 years ago by
Ram
45k • written 4.2 years ago by
smeeta
• 0
2
votes
1
reply
1.3k
views
command line VEP and VEP web interface return different results.
ensembl
vep
updated 4.2 years ago by
Emily
24k • written 4.2 years ago by
nhaus
▴ 420
0
votes
2
replies
1.2k
views
how to produce plot below using R
RNA-Seq
plot
circus
4.2 years ago by
adR
▴ 130
2
votes
1
reply
1.1k
views
DNA Methylome and RNA-seq intersect
RNA-seq
Methylome
DNA
updated 4.2 years ago by
Tian
▴ 50 • written 4.2 years ago by
Morris_Chair
▴ 370
0
votes
4
replies
1.5k
views
Can Omni-C reads be used for genome polishing?
Omni-C
polish
genome
4.2 years ago by
Biostar
• 0
1
vote
9
replies
3.3k
views
bioMart biotype assignment
biomart
4.2 years ago by
imaparna27
▴ 20
1
vote
6
replies
3.1k
views
How to Add FORMAT column from VCF file to table?
snp
vcftools
vcf
vep
updated 2.0 years ago by
Sanya
• 0 • written 4.2 years ago by
windsur
▴ 20
0
votes
5
replies
1.9k
views
BGZF file looks weird
BGZF
4.2 years ago by
HL
▴ 10
4
votes
1
reply
1.3k
views
IGV sequence name error .sam file
sam
graphmap
IGV
updated 4.2 years ago by
Antonio R. Franco
★ 5.2k • written 4.2 years ago by
A_heath
▴ 170
0
votes
0
replies
562
views
lncrna positive control gtex
gtex
lncrna
updated 4.2 years ago by
ATpoint
89k • written 4.2 years ago by
Taktak31
• 0
0
votes
0
replies
854
views
Need help interpreting CoGe SynMap result
genome
genomics
updated 2.6 years ago by
Ram
45k • written 4.2 years ago by
Lucas Peres
▴ 80
0
votes
0
replies
706
views
FISH Probe bed file
Vysis
Cytogenetics
FISH
4.2 years ago by
Jng
• 0
5
votes
4
replies
1.8k
views
Convert missing genotype ./. to homozygous 0/0 in vcf
vcf
updated 4.2 years ago by
sbstevenlee
▴ 480 • written 4.2 years ago by
User000
▴ 750
0
votes
6
replies
2.3k
views
How to convert gene names to GO term?
databse
4.2 years ago by
dpc
▴ 250
0
votes
1
reply
1.9k
views
bamdst gives error "EOF marker is absent. The input is probably truncated."
bwa
samtools
bamdst
updated 4.1 years ago by
aw7
▴ 390 • written 4.2 years ago by
shpak.max
▴ 60
0
votes
0
replies
676
views
Starting GWAS with Plink
GWAS
4.2 years ago by
dec986
▴ 380
0
votes
0
replies
641
views
How to find the genes within MetaCyc pathways?
database
4.2 years ago by
dpc
▴ 250
0
votes
0
replies
614
views
Longest common substring between two sequences with minimum error correction
algorithm
4.2 years ago by
Alex
• 0
0
votes
4
replies
2.4k
views
Cellranger-arc
cellranger
cellranger-arc
scRNA-seq
10x
4.2 years ago by
LacquerHed
▴ 30
0
votes
0
replies
1.1k
views
Job:
Program Manager - Computational Biology
Computational
Biosciences
Biology
4.2 years ago by
BerkeleyLab
▴ 70
1
vote
2
replies
1.2k
views
bcftools mpileup giving more wildtypes <*> than expected
bcftools
DNA-seq
mpileup
4.2 years ago by
gt
▴ 30
0
votes
1
reply
786
views
Annotating CNV
gnomad
Annotation
updated 4.2 years ago by
Ram
45k • written 4.2 years ago by
akshitiz09
▴ 20
0
votes
0
replies
773
views
freebayes only picking up variants in a single contig
variant-calling
DNA-seq
freebayes
4.2 years ago by
gt
▴ 30
2
votes
6
replies
2.3k
views
rMATS BAM file MemoryError Issue
rMATS
processing
BAM
4.2 years ago by
saipra003
▴ 20
0
votes
8
replies
2.9k
views
Error in DSSP Module of Biopython
Python
Biopython
4.2 years ago by
anasjamshed
▴ 140
0
votes
1
reply
704
views
Expression analysis of data obtained from Broad GDAC Firehouse (https://gdac.broadinstitute.org/)
gdac
tcga
updated 4.2 years ago by
Ram
45k • written 4.3 years ago by
jyotsnap
• 0
2
votes
0
replies
767
views
Herald:
The Biostar Herald for Tuesday, July 20, 2021
herald
4.2 years ago by
Biostar
3.6k
0
votes
3
replies
2.0k
views
error related to annovar software
rsid
annovar
VCF
SNP
4.2 years ago by
rheab1230
▴ 150
1
vote
2
replies
1.2k
views
retrieving entire genomic sequence contents of a database
genomes
mining
database
ftp
ensembl
updated 4.2 years ago by
Ben Moore
★ 2.4k • written 4.2 years ago by
saundythe8th
• 0
0
votes
0
replies
994
views
Does the normalization method affect scRNAseq data integration?
scran
scuttle
scRNAseq
integration
normalization
data
4.2 years ago by
joker33
▴ 150
3
votes
8
replies
2.5k
views
Spatial transcriptomics data
scalefactor
spatial
4.2 years ago by
lsudupe
▴ 20
9
votes
3
replies
1.6k
views
Forum:
How to manage Biostar email subscriptions?
biostars
updated 4.2 years ago by
natay
20 • written 4.2 years ago by
WUSCHEL
▴ 860
2
votes
3
replies
1.2k
views
Exons Distribution from single cell data.
exons
introns
scrna
updated 4.2 years ago by
benformatics
4.2k • written 4.2 years ago by
Cheng Wei
• 0
122,008 results • Page
611 of 2441
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Recommendations for 200 SNP markers genotyping
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Comment: DESeq2 on metagenome KO counts
by
ATpoint
89k
Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts
by
ATpoint
89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Answer: DESeq2 on metagenome KO counts
by
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3.9k
I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions: 1. All genes with t…
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(I apologise for my previous reply; I wanted to be as detailed as possible) DESeq2 handles KO counts perfectly well. For a time-series des…
Comment: DESeq2 on metagenome KO counts
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I apologise for how that sounded; I wanted to be as detailed as possible.
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A comment on: "*Wonky analysis is possible even with open-source R libraries.*" True - and arguably, the risk of a wonky analysis is actua…
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`Trailmaker` likely only supports Parse's evercode data. <br> `BioTuring` does not appear to have published pricing. <br> `Rosalind` appear…
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> I performed a standard proteomics screening workflow What database did you use to search against? Perhaps you are using an old (not so c…
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No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
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Wow, thats too long. How much RAM does your machine have, it is likely swapping
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Note that UniProtKB accession numbers do not have any meaning. While most ACs starting with A0A5* are indeed unreviewed (i.e. from TrEMBL),…
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Thank you but sorry, your answer sounds very AI-based...
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For basic analysis, discard anything that isn't from Swiss-Prot. Your statistics and pathway analysis should only be based on reliable, ann…
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