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121,912 results • Page
56 of 2439
Sort: Rank
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0
votes
0
replies
343
views
Packages for constructing Phylogenetic tree from HapMap file
HapMap
tree
Phylogenetic
SNP
10 months ago by
sujee119
• 0
3
votes
5
replies
3.3k
views
How Do I create a BED file from an hard masked fasta?
genome
sequencing
updated 10 months ago by
hewm2008
▴ 50 • written 6.3 years ago by
marcofraca
▴ 20
3
votes
1
reply
733
views
What is the reason that all high throughput sequencing data for the human brain is snRNA-seq instead of scRNA-seq ?
10x
scanpy
python
single-cell
anndata
updated 10 months ago by
jared.andrews07
★ 19k • written 10 months ago by
AlexStar
▴ 200
1
vote
2
replies
630
views
Picard LiftoverVCF Maps Variants to Incorrect Chromosomes When Processing Individual Chromosomes
liftovervcf
10 months ago by
jonas.andersson
▴ 40
0
votes
0
replies
428
views
News:
Master Evidence Synthesis with Meta-analysis in R (Online Course - Feb 10-14, 2025)
Meta-analysis
Review
Evidence-Synthesis
10 months ago by
Physalia-courses
★ 2.6k
0
votes
3
replies
762
views
PCA plot
fviz_pca
factoextra
updated 10 months ago by
Bastien Hervé
6.5k • written 10 months ago by
4732b159
• 0
6
votes
8
replies
1.7k
views
NGS data analysis
NGS
eukaryotic
10 months ago by
Acervo
• 0
0
votes
0
replies
352
views
Intersect between bedGraph and bed file
count
bedtools
bedGraph
Matrix
10 months ago by
daffodil
▴ 10
1
vote
0
replies
518
views
is there any data base or reference to provide a comprehensive list of CD marker expression in different white blood cell types?
DEG
myeloid
CDmarker
leukocyte
10 months ago by
qasemi.m.q
▴ 10
1
vote
2
replies
950
views
How to interpret that overrepresented and duplicate sequences influence %GC content?
Duplicates
FASTQC
MultiQC
Fastq
GC
10 months ago by
tvibhaps
▴ 10
0
votes
0
replies
359
views
Should we normalize/transform WGBS beta values?
normalization
WGBS
methylation
transfromation
10 months ago by
Lalaland
▴ 40
0
votes
4
replies
1.0k
views
What is the best way to confirm if a mutated gene is more frequent in recurrence group than in baseline?
statistics
compare_groups
gene_count
10 months ago by
Lila M
★ 1.3k
0
votes
0
replies
361
views
How to combine replicates in profile plot in profileplyr package?
ATAC-Seq
profilePlot
profilePlyr
updated 10 months ago by
GenoMax
153k • written 10 months ago by
B.N.
▴ 10
0
votes
2
replies
1.0k
views
No Cluster ID's present when making UMAP for Joint RNA and ATAC analysis: Signac 10x multiomic tutorial
multiomics
snATACseq
snRNAseq
10 months ago by
bgbs
• 0
0
votes
0
replies
322
views
Phasing alleles with SHAPEIT4: cases and controls together or separately?
cases-controls
separately
together
case-control
phasing
10 months ago by
igor.alcaras
• 0
2
votes
1
reply
2.1k
views
Is it better to phase two populations together or separately?
phasing
beagle
populations
updated 10 months ago by
igor.alcaras
• 0 • written 9.9 years ago by
eyb
▴ 270
2
votes
8
replies
1.8k
views
SRAtoolkit --split-files output
sratoolkit
sra
fastq
10 months ago by
tony_88888
• 0
0
votes
0
replies
467
views
database of gmap file for GLIMPSE2 imputation
gmap
GLIMPSE2
10 months ago by
cautree
• 0
3
votes
6
replies
1.7k
views
Create a fasta and gtf file
gtf
human
genome
fasta
updated 10 months ago by
Juke34
9.3k • written 10 months ago by
ATRX
★ 1.2k
1
vote
2
replies
734
views
Regarding to Two-color microarray data analysis (DGE)
Differential-expression-analysis
updated 10 months ago by
Ram
45k • written 10 months ago by
SHIRUI
▴ 10
11
votes
12
replies
2.6k
views
dedup STAR transcriptome file using umi_tools
rna-seq
umi
transcriptome
umi_tools
10 months ago by
ATRX
★ 1.2k
0
votes
1
reply
527
views
ChIP-seq signal values
values
chipseq
signal
updated 10 months ago by
1769mkc
★ 1.3k • written 10 months ago by
sk_24
▴ 10
0
votes
0
replies
386
views
Speclib of Rattus novergicus (taxid 10116) to use in DIA-NN
Proteomics
10 months ago by
thalisommoreiraskt
• 0
0
votes
1
reply
627
views
News:
[Survey] Help Shape the Future of Genomic Data Storage Solutions!
genomics
bioinformatics
survey
solutions
storage
updated 10 months ago by
Michael
56k • written 10 months ago by
spacecow
• 0
1
vote
1
reply
464
views
QQ plot with small bump in the middle
QQ-plot.GWAS
updated 10 months ago by
Ram
45k • written 10 months ago by
zhuzhu
▴ 10
4
votes
3
replies
1.4k
views
Confused by reference files
reference
alignment
updated 10 months ago by
GenoMax
153k • written 10 months ago by
Nesma
• 0
3
votes
4
replies
1.0k
views
Contrasts for comparing condition within tissue
limma
deseq2
edgeR
contrasts
updated 10 months ago by
SamGG
▴ 150 • written 10 months ago by
Ben
▴ 30
1
vote
2
replies
791
views
How to Map NCBI taxid to Open Tree of Life ott_id Without Using Scientific Names?
taxonomy
ott
10 months ago by
Martín Ezequiel
• 0
0
votes
2
replies
776
views
Cellranger: Demux pooled (hashing antibodies) GEX and VDJ 10x sequence fastq data
hashing
cellranger
demux
10 months ago by
Flipstone
• 0
0
votes
0
replies
395
views
Fixed peak width in ENCODE TFs ChIP-seq
MACS2
ChIP-seq
ENCODE
10 months ago by
DavideBrex
▴ 20
0
votes
0
replies
372
views
vg call AD frequencies for certain sites
vg
10 months ago by
Danny
• 0
2
votes
2
replies
1.3k
views
Job:
Research Scientist - Bioinformatics position in Milan, Italy
R
Python
RNASeq
singleCell
10 months ago by
kanika.151
▴ 160
0
votes
3
replies
763
views
Questions about finding similar genes and dissimilar genes in BLAST
E-value
similarity
BLAST
updated 10 months ago by
biofalconch
★ 1.3k • written 10 months ago by
William
• 0
1
vote
3
replies
1.8k
views
Question about variant calling method using pangenome-graph
vg
updated 10 months ago by
Jouni Sirén
▴ 760 • written 10 months ago by
Marion
• 0
0
votes
1
reply
536
views
Are there specific pipelines for identifying solo-TIRs?
solo-TIR
elements
transposable
updated 10 months ago by
biofalconch
★ 1.3k • written 10 months ago by
Marcos
▴ 10
3
votes
5
replies
1.5k
views
Optical Duplicates
gatk
MarkDuplicates
optical-duplicates
updated 10 months ago by
Ram
45k • written 10 months ago by
ebogen
▴ 10
4
votes
2
replies
863
views
Tool:
A notebook for checking relatedness and X heterozygosity from sequencing data
heterozygosity
relatedness
sequencing
sex
estimation
10 months ago by
barslmn
★ 2.4k
0
votes
0
replies
511
views
Signac for mgatk scRNA-seq data
mgatk
Signac
scRNA-seq
10 months ago by
marco.barr
▴ 180
0
votes
0
replies
420
views
Homer annotatePeaks.pl output
start
annotatePeaks.pl
chr
homer
position
updated 10 months ago by
GenoMax
153k • written 10 months ago by
Rakesh
• 0
1
vote
2
replies
700
views
Extract gene_id and protein_id from .gtf file to create a list with them
gtf
bash
protein_id
10 months ago by
Eduardo Oñate
• 0
0
votes
0
replies
397
views
GEOquery getGEO is normalized data or not?
getgeo
geoquery
microarray
10 months ago by
tyasird
▴ 10
27
votes
35
replies
5.4k
views
Indexing a 2.6GB Plant Genome Using STAR (genomeGenerate Mode) Terminated Due to RAM Limit — Can the Genome Be Split for Indexing, or Are There Other…
star
RAN-seq
bam
genome
indexing
updated 10 months ago by
Dunois
★ 2.9k • written 10 months ago by
Vijith
▴ 100
1
vote
3
replies
860
views
Tool:
I Built a Simple Website to Help Researchers find Research Grants
web-application
grants
research
funding
updated 10 months ago by
GenoMax
153k • written 10 months ago by
bitsofadventures
▴ 40
4
votes
1
reply
635
views
Differential Expression Analysis with only one replicate
Differential-Expression-analysis
updated 10 months ago by
Ram
45k • written 10 months ago by
ZuelTech
• 0
4
votes
7
replies
1.5k
views
Basic de novo assembly of plant genome
Assembly
updated 10 months ago by
lieven.sterck
15k • written 10 months ago by
Lemonhope
▴ 10
0
votes
4
replies
1.2k
views
TCGAbiolinks - fewer samples than expected
TCGABiolinks
TCGA
updated 10 months ago by
Zhenyu Zhang
★ 1.3k • written 14 months ago by
elmira.yazdii
• 0
2
votes
4
replies
900
views
NCI Genomic Data Commons gdc-rnaseq-tool
RNA-seq
Genomic-Data-Commons
10 months ago by
cthangav
▴ 110
1
vote
6
replies
1.7k
views
count number of polymorphic sites among samples in vcf
bcftools
vcf
10 months ago by
vaellis
• 0
1
vote
2
replies
853
views
Using Lordec to correct Nanopore DRS reads
lordec
nanopore
read-correction
10 months ago by
baibhu1234
▴ 60
0
votes
1
reply
636
views
Genetic modification in mosquito sequence
gene-modification
crispr
ncbi
updated 10 months ago by
Ram
45k • written 10 months ago by
sugamohanasundaram
• 0
121,912 results • Page
56 of 2439
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Answer: Different UMAP for batch correction in R and Pytho
Answer: Different UMAP for batch correction in R and Pytho
Answer: Different UMAP for batch correction in R and Pytho
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Answer: Different UMAP for batch correction in R and Pytho
Answer: WGCNA package in R: dendogram plot error
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq
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Comment: [vg giraffe] Unable to add read group to BAM file
by
saruman
• 0
It seems that using the following format fixes the problem: --read-group "1 SM:HG002 LB:lib1 PL:illumina PU:unit1" As shown below: …
Comment: Developing a genomics ML model using bytes?
by
dariober
15k
> what if we can use the bytes to develop a model? My understanding is that the OP is considering building a model using the sequences in …
Comment: WGCNA package in R: dendogram plot error
by
RJ
• 0
You might had delete the outliers from the expression table but then the traits data.frame doesn't match with expression table dimensions.
Comment: miRNA low mapping ratings
by
Ant
▴ 50
No, it's a personal dataset. I haven’t seen the link, but if I understand correctly, it's not possible to use the software for free, right?
Comment: miRNA low mapping ratings
by
GenoMax
153k
So this is a public dataset? QIAseq miRNA libraries may require special handling. Have you seen --> https://resources.qiagenbioinformatics.…
Comment: Trouble when installing arb
by
GenoMax
153k
Are you referring to software found here --> http://download.arb-home.de/release/latest/ ? If so why are you installing the source. Authors…
Comment: Hifiasm is getting killed while trying to assemble a genome
by
GenoMax
153k
All valid points. This is a SRA dataset. If it is covered by a publication hopefully it is not a bad one. @Pranav if you can post the SRA a…
Answer: Different UMAP for batch correction in R and Pytho
by
antonioggsousa
3.4k
Hi, I'm mostly an R user, but the codes you presented look correct to me. The two UMAP projections *"look too similar to be different"*, …
Answer: How to properly assemble phage genomes?
by
Joe
22k
This might help: https://millardlab.org/lab-members/alumni/lucy-gannon/lucys-beginner-guide-to-bacteriophage-genome-assembly/
Comment: RNA-SEQ where only a subset of genes is of interest
by
piffelpaff
• 0
Thanks for your reply. Yes it's single-cell and we're talking about roughly 30 pre-selected genes. I see. I was rather referring to the d…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple
by
Joe
22k
This may not be exactly what you're looking for (kind of the other way around, predicting synthetic clusters from genes rather than the pro…
Comment: Developing a genomics ML model using bytes?
by
ATpoint
89k
How is this different from https://www.biostars.org/p/9615062/
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq
by
npb27
▴ 20
Hi thanks for your answer Interesting idea about ribosome length, although I can't think why this should affect the apparent 3' position b…
Comment: RNA-SEQ where only a subset of genes is of interest
by
ATpoint
89k
Is this single-cell? How many genes are we talking about? > The alternative would be to just use the raw data without normalization, run W…
Comment: Developing a genomics ML model using bytes?
by
ATpoint
89k
So essentially you work on a compression algorithm, is it? If so, be sure to bechmark your idea against the hundreds of existing and fast c…
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