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121,912 results • Page
54 of 2439
Sort: Rank
Rank
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Votes
Replies
1
vote
1
reply
846
views
CNVKit batch output
CNVkit
deletion
duplication
updated 10 months ago by
Eric T.
★ 2.9k • written 11 months ago by
aLex97
• 0
0
votes
0
replies
264
views
Interpreting Pathway 7049: Fatty Acid Salvage in PICRUSt2 Results from Nephele
PICRUSt
10 months ago by
benkosta
• 0
1
vote
3
replies
1.0k
views
I encountered some problem while using bitr() for gene ID transversion.
bioMart
10 months ago by
Pallondyle
• 0
0
votes
0
replies
364
views
Include NCBI taxonomic ID (txid) in the header of downloaded sequences using Biopython
taxonomy
sequences
Biopython
ncbi
10 months ago by
Martín Ezequiel
• 0
0
votes
1
reply
708
views
Best Transcriptome file for Salmon after STAR alignment
fasta
salmon
star
rna-seq
alignment
updated 10 months ago by
biofalconch
★ 1.3k • written 10 months ago by
rayanelkholdi
• 0
0
votes
0
replies
563
views
ClusterProfiler GO / KEGG enrichment analysis for non Model organism
KEGG
RNA-SEQ
enrichemnt
9 months ago by
Pegasus
▴ 130
1
vote
2
replies
838
views
Do I need to regressout uninteresting sources of variation bebofe pseudobul DESeq2 differential expression analysis in single cell data
scRNA-seq
regression
DESeq2
pseudobulk
updated 10 months ago by
Ram
45k • written 10 months ago by
alvaroperona1
• 0
0
votes
0
replies
329
views
Performing Differential Analysis with NarrowPeak Files in ATAC-seq: Tumour vs. Control
R
Differential-Analysis
NarrowPeak
ATAC
updated 10 months ago by
Ram
45k • written 10 months ago by
Thom
• 0
1
vote
10
replies
3.4k
views
Question about CIBERSORTx Docker to Singularity
CIBERSORTx
docker
singularity
updated 10 months ago by
Jose
• 0 • written 15 months ago by
jinghuang800
▴ 10
0
votes
0
replies
342
views
specificity of pathway enrichment
pathway-enrichment
Gene-ontology
updated 10 months ago by
Ram
45k • written 10 months ago by
hubsnets
▴ 30
0
votes
0
replies
692
views
Changing Cellchat labels or group.by function
Cellchat
10 months ago by
odi
▴ 10
1
vote
3
replies
1.6k
views
Deseq2 output and robust PCA (PcaGrid and PcaHubert)
rPca
Deseq2
RNA-seq
cPca
updated 7 months ago by
Guoyan
• 0 • written 20 months ago by
Emma
• 0
0
votes
0
replies
353
views
Building design matrix for scRNAseq experiment
differential-gene-expression
scRNAseq
MAST
updated 10 months ago by
Ram
45k • written 10 months ago by
merdanosman
• 0
0
votes
1
reply
732
views
conorm warning in python
python
rnaseq
conorm
updated 10 months ago by
Mensur Dlakic
★ 30k • written 10 months ago by
Shaimaa Gamal
▴ 10
10
votes
5
replies
2.7k
views
What is the difference between `possorted_genome_bam.bam` in the output of `cellranger count` and `sample_alignments.bam` in the output of `cellrange…
velocity
RNA-seq
single-cell
updated 10 months ago by
Ram
45k • written 2.5 years ago by
Dan
▴ 180
0
votes
7
replies
1.5k
views
How to handle duplicate genes in DoHeatmap() for top DEGs across clusters (seurat single cell)
seurat
updated 10 months ago by
Bastien Hervé
6.5k • written 10 months ago by
Picasa
▴ 690
0
votes
3
replies
1.3k
views
How to update ncbi-blast+?
blast
updated 10 months ago by
GenoMax
153k • written 10 months ago by
ongchip
• 0
2
votes
4
replies
796
views
Wilcox or T-test with percentages in R
R
updated 10 months ago by
michael.ante
★ 4.0k • written 10 months ago by
Nona
▴ 90
1
vote
3
replies
1.1k
views
how to run limma for large datasets
R
HPC
biostatistics
statistics
updated 10 months ago by
Gordon Smyth
★ 8.3k • written 18 months ago by
Bioinfonext
▴ 480
3
votes
7
replies
1.3k
views
[construct a model.matrix ]
regression
lm
methylation
model_matrix
updated 10 months ago by
Dunois
★ 2.9k • written 10 months ago by
kyj222637
▴ 10
0
votes
2
replies
1.2k
views
Error 137 in Epi2me TB-AMR Workflow
amr
ont
epi2me
pipeline
tb
updated 10 months ago by
jared.andrews07
★ 19k • written 10 months ago by
End
• 0
1
vote
4
replies
1.0k
views
Best way of visualzing RNA-seq bam files
IGV
10 months ago by
ATRX
★ 1.2k
0
votes
3
replies
766
views
Help with finding scRNA-seq data
10x
scanpy
python
single-cell
anndata
updated 4 months ago by
ehaag
▴ 100 • written 10 months ago by
AlexStar
▴ 200
0
votes
4
replies
1.2k
views
Comparing two RNA-seq runs (each has enough replicates) in DESeq2
DESeq2
updated 10 months ago by
james.hawley
▴ 80 • written 10 months ago by
bibrgr
• 0
5
votes
9
replies
2.0k
views
bcl2fastq
bcl2fastq
bcl
fastq
lane
updated 10 months ago by
GenoMax
153k • written 10 months ago by
kilcdincer
▴ 10
0
votes
2
replies
808
views
How to perform corrected Cell Barcode/UMI calling with an externally sorted BAM?
bam
alignment
starsolo
star
updated 10 months ago by
dsull
★ 7.7k • written 10 months ago by
mk
▴ 310
1
vote
1
reply
795
views
Missing Transcripts in StringTie GTF Output Affecting Downstream Analysis with prepDE.py
prepDE.py
Stringtie
updated 10 months ago by
lieven.sterck
15k • written 10 months ago by
upretia
• 0
2
votes
2
replies
750
views
Bowtie2 not aligning read...but should?
bowtie2
updated 10 months ago by
GenoMax
153k • written 10 months ago by
theclubstyle
▴ 40
0
votes
0
replies
418
views
AAI matrix with compareM
AAI
matrix
10 months ago by
anna
• 0
8
votes
15
replies
7.1k
views
12 follow
ADMIXTURE Segmentatio fault
admixture
plink
vcf
updated 4 months ago by
Mwangana
• 0 • written 4.3 years ago by
pmc.sa
▴ 40
2
votes
5
replies
1.5k
views
Handling Negative Values in Log-Transformed a Dataset for Differential Expression Analysis with Limma
microarray
updated 10 months ago by
Gordon Smyth
★ 8.3k • written 10 months ago by
Maryam
• 0
2
votes
3
replies
962
views
Full length 18S rRNA data from Nanopre
Linux
updated 10 months ago by
1769mkc
★ 1.3k • written 10 months ago by
Adyasha
• 0
8
votes
3
replies
1.2k
views
What's going on with Ensembl?
biomaRt
ensembl
updated 10 months ago by
Louisse_Ensembl
▴ 170 • written 10 months ago by
yura.grabovska
▴ 820
2
votes
4
replies
1.6k
views
Error in biomaRt useMart and useDataset accessing ovis aries genome
biomaRt
updated 10 months ago by
Louisse_Ensembl
▴ 170 • written 11 months ago by
Michael
• 0
0
votes
3
replies
1.1k
views
PCA Plotting Differences Before and After Batch Correction in RNA-seq for Meta-Analysis
batch
RNA-seq
correction
PCA
updated 10 months ago by
Basti
★ 2.1k • written 10 months ago by
Nelo
▴ 20
1
vote
2
replies
1.3k
views
How to install deconstructSigs in R
R
updated 10 months ago by
ATpoint
89k • written 10 months ago by
Zhenyu Zhang
★ 1.3k
0
votes
1
reply
737
views
Is there a function in cytoscape for calculating node strength ?
network
cytoscape
igraph
updated 10 months ago by
Scooter
▴ 310 • written 10 months ago by
SplitInf
▴ 20
0
votes
1
reply
551
views
CRISpick github/downloadable local copy
CRISPR
CRISPRai
CRISpicj
updated 10 months ago by
GenoMax
153k • written 10 months ago by
noodle
▴ 650
1
vote
0
replies
943
views
How to create a signature matrix, using scRNA-seq data, for downstream CIBERSORTx deconvolution of bulk data when the data is too heavy?
CIBERSORTx
deconvolution
Seurat
scRNA-seq
bulkRNA-seq
10 months ago by
Fossil
▴ 30
0
votes
0
replies
351
views
Single-Cell RNA Sequencing: Find Tissue with Highest Sox1 Expression
RNA-Seq
10 months ago by
Koki
• 0
2
votes
2
replies
945
views
Method to detect CNV in a large set of coverage profile ?
bam
cnv
coverage
machine-learning
updated 10 months ago by
jared.andrews07
★ 19k • written 10 months ago by
Pierre Lindenbaum
166k
1
vote
0
replies
550
views
Blog:
How to create Sunburst plot using echarts4r R package or sunburstR package for categorical data of Dengue
echarts4R
sunburstR
10 months ago by
rohitsatyam102
▴ 940
1
vote
0
replies
339
views
How to create scoring file with LDpred2?
PGS
Scoring
LDpred2
Beta
10 months ago by
d0gs_
▴ 10
6
votes
7
replies
1.1k
views
Changing label geom_text in ggplot
ggplot
10 months ago by
Nona
▴ 90
1
vote
2
replies
764
views
gWidgets2RGtk2 problem for newer versions of R
data-science
gWidgets2RGtk2
rstudio
r
updated 10 months ago by
tothepoint
▴ 940 • written 10 months ago by
burak
• 0
1
vote
2
replies
756
views
spatial transcriptomic and protemomic
spatial
transcriptomic
10 months ago by
Synat
• 0
0
votes
0
replies
836
views
Job:
Bioinformatician at Max Planck Institute for plant breeding research (Cologne, Germany)
bioinformatician
MPIPZ
opening
10 months ago by
microfuge
★ 2.0k
4
votes
2
replies
1.2k
views
Job:
Experienced Bioinformatician Seeking Opportunities in NGS Data Analysis and Pipeline Development
Pipeline-Development
NGS
Genomics
Transcriptomics
Data-Analysis
6 months ago by
Bernard
▴ 30
0
votes
1
reply
547
views
Best Differential Abundance Tool for Microbiome Studies and Ensuring Cross-Study Comparability
abundance
differential
10 months ago by
benkosta
• 0
1
vote
2
replies
1.2k
views
Job:
finding jobs in bioinformatics
jobs
searching
10 months ago by
Sam
• 0
121,912 results • Page
54 of 2439
Recent Votes
A: How to extract reads with no INDEL?
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
Answer: Tried building a compact sequence format with 4-bit storage
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: RNA-SEQ where only a subset of genes is of interest
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Recent Replies
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…
Comment: How to get a legend from genoplotR?
by
antonioggsousa
3.4k
Hi, I'm not familiar with this package or function, but from the function documentation that you had provided in the link, it says about …
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