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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
0
replies
66
views
KissDE and batch effect
kissDE
kissplice
3 days ago by
david.b.rombaut
▴ 10
0
votes
1
reply
105
views
Zenodo command line uploads
zenodo
updated 2 days ago by
Arup Ghosh
3.0k • written 3 days ago by
zhousun21
▴ 40
0
votes
3
replies
148
views
CD4+ and CD8+ T cell classification
Immunology
T
cell
updated 3 days ago by
antonioggsousa
★ 2.5k • written 4 days ago by
pgangaitkar
• 0
0
votes
0
replies
73
views
filtering exonic variants from the annoated file
Filtering
snpEff
annotation
4 days ago by
maajid
• 0
0
votes
0
replies
80
views
Create UPGMA tree
TREE
SNP
UPGMA
R
GDS
4 days ago by
rjsgur789
• 0
0
votes
1
reply
97
views
Converting RSIDs in the HLA region (e.g.) HLA-A*:01:01g-B*08:01 format?
SNP
HLA
rsid
updated 3 days ago by
GenoMax
119k • written 4 days ago by
4galaxy77
★ 2.2k
0
votes
0
replies
93
views
Signac peak sorting
scATAC-seq
seurat
signac
4 days ago by
rbronste
▴ 400
0
votes
0
replies
66
views
cgMLST
MLST
4 days ago by
Ahmed Allam
• 0
0
votes
0
replies
115
views
checking allelic expression from SNP showing both Biallelic and monoallelic expression for sample gene
Single-Cell-RNA-seq
SNP
RNA-Seq
ASEreadcounter
allelic
4 days ago by
luckysardar171
▴ 20
0
votes
0
replies
106
views
inquiry related to gtex normalization
gtex
normalization
gene
count
4 days ago by
rheab1230
▴ 60
0
votes
0
replies
113
views
snpEff problems adding regulatory regions to database
snp
snpEff
gwas
TFBS
4 days ago by
mcsimenc
▴ 20
2
votes
0
replies
102
views
Composition-Conditioned-CrystalGAN
gans
proteinstructure
proteinfolding
pytorch
4 days ago by
Wiktoria
▴ 20
1
vote
1
reply
134
views
SQL query to find all specific value in all columns based on row id.
sql
updated 4 days ago by
Pierre Lindenbaum
147k • written 4 days ago by
lippithakkar
• 0
0
votes
0
replies
91
views
Signac MACS2 peak shape question
snATAC-seq
snRNA-seq
signac
multiome
seurat
4 days ago by
rbronste
▴ 400
0
votes
0
replies
76
views
D-loop in mitogenomes?
gene
genome
protein
4 days ago by
sunnykevin97
▴ 970
0
votes
0
replies
79
views
PennCNV-Seq
command
PennCNV-Seq
execute
the
4 days ago by
heureuse
• 0
1
vote
1
reply
111
views
Downloading Data from ICGC via Amazon AWS EC2
ICGC
Token
updated 4 days ago by
GenoMax
119k • written 4 days ago by
Hashirama
▴ 20
0
votes
0
replies
71
views
ASCAT + ShallowHRD
using
status
HRD
ShallowHRD
4 days ago by
shounak.chakraborty1990
▴ 20
0
votes
0
replies
65
views
Classify unknown TEs produced by RepeatModeler
repeats
TE
genome
4 days ago by
kirillkirilenko.tomsk
• 0
0
votes
2
replies
148
views
phylogeny
phylogeny
genes
with
virulence
3 days ago by
saifulislam99121
• 0
0
votes
0
replies
78
views
Download specific sequences from databases using a Ruby-Script
KEGG
Ruby
database
5 days ago by
Theresa
• 0
0
votes
0
replies
82
views
facing difficulty while interpreting mean-variance trend plot in GEO2R
GEO2R
normalization
mean-variance
GEO
5 days ago by
ElfoHelpo
• 0
0
votes
0
replies
68
views
Fetching schemes from pubMLST
Fetching
pubMLST
schemes
cgMLST
scheme
5 days ago by
davidmaimoun
▴ 50
0
votes
1
reply
101
views
liftover bed not matching panel gene names
liftover
vcf
bed
bedtools
5 days ago by
whb
▴ 30
0
votes
3
replies
292
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
normalization
batcheffect
single_cell_features
training_test_split
4 days ago by
mmitra
▴ 40
0
votes
1
reply
161
views
STAR fails: quality string length is not equal to sequence length but only AFTER cutadapt is run
fastq
cutadapt
rna-seq
STAR
updated 5 days ago by
ATpoint
64k • written 5 days ago by
bioinfo_cat
• 0
0
votes
0
replies
101
views
UK Biobank vs. NIH-EBI GWAS catalogue
UK
Biobank
GWAS
NIH-EBI
5 days ago by
Sanjar
▴ 140
0
votes
4
replies
236
views
CPTAC data download, transcriptomics
CPTAC
download
data
transcriptome
4 days ago by
Rob
▴ 130
1
vote
1
reply
144
views
Determining strandedness of RNAseq samples from count data and understanding counts in sex genes
strandedness
htseq
RNAseq
updated 5 days ago by
ATpoint
64k • written 5 days ago by
sr41489
• 0
0
votes
1
reply
126
views
VCF to MAF using oncotator
vcf
maf
oncotator
to
updated 4 days ago by
Dave Carlson
▴ 890 • written 5 days ago by
hamrejr
• 0
0
votes
0
replies
87
views
How can one identify genome segments and mutations in Influenza viruses?
Bioinformatics
influenza
viruses
5 days ago by
eennadi
▴ 20
0
votes
0
replies
97
views
One-to-many pairwise alignment
pairwise
alignment
6 days ago by
Xiaokang
▴ 70
0
votes
0
replies
183
views
How to analyse .cdf or .mzML raw mass spectrometry files to get relative abundances of compounds in metabolome?
mass
spectrometry
data
metabolome
analysis
6 days ago by
dpc
▴ 240
1
vote
0
replies
110
views
r package for downstream analysis of phylogenetic trees
phylogenetics
R
6 days ago by
TM
▴ 10
0
votes
0
replies
99
views
any way to merge functions of kegg orthologs database?
functional-profile
metagenomics
data-wrangling
6 days ago by
v.berriosfarias
▴ 60
0
votes
0
replies
142
views
Package suggestion to calculate Protein-Protein interaction.
Free
FoldX
Binding
Affinity
Interaction
Energy
Protein-Protein
6 days ago by
UGUR
• 0
0
votes
1
reply
201
views
What does adjusted p value mean in GO overrepresentation analysis? [clusterProfiler]
clusterProfiler
updated 6 days ago by
4galaxy77
★ 2.2k • written 6 days ago by
Deepblue
▴ 10
0
votes
1
reply
155
views
Variant Effect Predictor (VEP) warning on insertions: coordinates are not (start = end + 1)
VCF
VEP
updated 6 days ago by
Pierre Lindenbaum
147k • written 6 days ago by
beketamas
• 0
0
votes
0
replies
136
views
Pairwise alignment of two long chromosomes (~100Mbp) with lastz
long
aligning
lastz
6 days ago by
vahe.galstyan
• 0
0
votes
0
replies
110
views
exploring genetic differences among highly close populations
gene
snp
population
6 days ago by
yzko
• 0
0
votes
0
replies
118
views
Whole genome sequence data - plotting chromosome position in R -windows11?
data.
WGS
balance
allelic
plot
6 days ago by
H_variant1
• 0
0
votes
0
replies
110
views
calculate meandepths for CDSs after mapping transcriptome reads to the genome
gtf
sam
meandepth
samtools
alignment
3 days ago by
poecile.pal
▴ 40
3
votes
2
replies
208
views
Feature selection for a binary classifier using mixed cancer type samples
genes
training-test
mixed
samples
split
feature
DE
selection
classifier
6 days ago by
mmitra
▴ 40
0
votes
0
replies
143
views
How to find variant frequency of nonsynonymous mutations using R?
variant
frequency
7 days ago by
ashaji
• 0
0
votes
0
replies
119
views
How might I downsample clustered data in the most representative way?
rep-seq
IgPhyML
clustering
downsample
trees
7 days ago by
Jesse
▴ 170
0
votes
3
replies
288
views
How to add name to Fasta header
python
updated 7 days ago by
GenoMax
119k • written 9 days ago by
ledba
• 0
0
votes
0
replies
111
views
Crunch file for Artemis Comparison Tool
WGS
ACT
Artemis
7 days ago by
SushiRoll
• 0
0
votes
0
replies
121
views
Correlation Plot of Two Biological Replicates of GRO-seq Data
groHMM
GRO-seq
HOMER
7 days ago by
LDT
▴ 40
0
votes
3
replies
199
views
OrthomclLoadBlast: I am not getting the log file or SimilarSequences table.
mysql
Orthomcl
updated 7 days ago by
GenoMax
119k • written 8 days ago by
vasundharak
• 0
0
votes
0
replies
142
views
blast ring image generator PROBLEM
genome
visualization
mapping
8 days ago by
Максим
• 0
1,000 results • Page
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Recent Votes
Answer: fgsea
Answer: Finding out if a query sequence is present in a read library / bam file (blast a
C: GTF based salmon index file for GRCh38
C: GTF based salmon index file for GRCh38
Answer: Has anybody managed to install and run GroopM lately?
How to integrate multiple data sets from microarray platform prior meta-analysis?
How to integrate multiple data sets from microarray platform prior meta-analysis?
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Comment: The best way to get gene lengths for 15K+ genes?
by
rpolicastro
9.4k
You should first ensure that calculating TPMs like this is valid for your analysis. Proper TPMs generally need to be calculated from transc…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴ 10
Hey! I tried the script, but I am getting this error: > SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaultin…
Comment: Expanding reference genome with alt loci and decoy sequences
by
appropiate
▴ 30
My criteria for whether it makes sense would be comparing MAPQ values for alignments when using reference genome vs expanded genome. If the…
Comment: Warning - longer object length is not a multiple of shorter object length
by
JACKY
▴ 10
Thanks! Do you also think my genelength calculation method is slumpy? What do you think about this approach? library (EDASeq) en…
Answer: Does Cellranger filter out doublet?
by
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64k
FAQ: https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-
Comment: Expanding reference genome with alt loci and decoy sequences
by
ATpoint
64k
Yes, technically you can append any sequence to the reference followed by building a new index. If that makes sense or is appropriate is a …
Comment: Warning - longer object length is not a multiple of shorter object length
by
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52k
for example edgeR see https://support.bioconductor.org/p/64585/ Refer to https://www.biostars.org/p/115674/ , https://www.ncbi.nlm.nih.go…
Answer: How to insert dbSNP in a database?
by
Pierre Lindenbaum
147k
1) why do you need this ? 2) you can always upload the UCSC dbsnp files. ex.: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/databas…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴ 10
thanks! I will try it out today
Comment: getting RPKM and VST using DEseq2 package
by
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6.4k
Check out [this][1] discussion on gene length in DESeq2. [1]: https://support.bioconductor.org/p/67131/
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▴ 10
A proven Bioconductor package you mean using a package for normalization? If so, is there any package you recommend ?
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Did you adjust this setting in the maker_opts.ctl file? >pred_stats=1 #report AED and QI statistics for all predictions as well as models
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Sorry, I haven't tried this myself because I don't have a running braker pipeline myself yet. There are two possibilities, either Braker ge…
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Hey you can use stlearn package in Python, create an ANN object manually using function >ann_object = st.create_stlearn(count=count_matri…
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Is there a script that automatically inserts this image each time `Excel` or `excel` are mentioned in a message? If so, hopefully you will …
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