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566 results • Page
3 of 12
Sort: Rank
Rank
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Votes
Replies
0
votes
1
reply
147
views
Seurat: How to get all genes name of a cell ?
seurat
updated 7 days ago by
jv
★ 1.2k • written 8 days ago by
Picasa
▴ 640
1
vote
0
replies
234
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 7 days ago by
Ram
39k • written 8 days ago by
Supernova
• 0
0
votes
0
replies
103
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 7 days ago by
Ram
39k • written 8 days ago by
Fred
• 0
2
votes
2
replies
119
views
how to use Hemtools bed2vcf?
vcf
linux
conversion
bed
updated 8 days ago by
Pierre Lindenbaum
154k • written 8 days ago by
MobiusT
▴ 10
0
votes
1
reply
151
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 7 days ago by
Ram
39k • written 8 days ago by
chengc2016zzu
• 0
0
votes
0
replies
85
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
8 days ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
207
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
7 days ago by
Pegasus
▴ 90
0
votes
0
replies
121
views
Merging multiple PLINK files
plink
merging
8 days ago by
Nejla
• 0
0
votes
0
replies
119
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 8 days ago by
GenoMax
129k • written 8 days ago by
keiko.asakura
• 0
0
votes
2
replies
226
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
7 days ago by
J.F.Jiang
▴ 900
0
votes
2
replies
206
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 8 days ago by
Ram
39k • written 9 days ago by
Joel Wallenius
▴ 130
1
vote
3
replies
704
views
Regular Expression for conversion
Linux
grep
updated 7 days ago by
Joe
21k • written 20 months ago by
shabbas12
▴ 10
0
votes
1
reply
172
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 7 days ago by
Ram
39k • written 9 days ago by
barrypraveen
▴ 110
0
votes
2
replies
178
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
9 days ago by
pg45863
• 0
0
votes
1
reply
140
views
ABySS Process Killed
ABySS
genome
assembly
updated 9 days ago by
GenoMax
129k • written 9 days ago by
asarcillo
• 0
0
votes
0
replies
101
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
9 days ago by
narges.bioinf
• 0
0
votes
3
replies
230
views
Query qbout single cell sequencing
fastq
ScRNA
updated 7 days ago by
Ram
39k • written 9 days ago by
abbas.waseem.gcu
▴ 20
0
votes
1
reply
189
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 8 days ago by
fracarb8
▴ 950 • written 9 days ago by
Sun
• 0
0
votes
1
reply
181
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 9 days ago by
Pierre Lindenbaum
154k • written 9 days ago by
MobiusT
▴ 10
0
votes
4
replies
293
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
9 days ago by
Ahmad
▴ 10
0
votes
2
replies
252
views
Error in download library file in expression console software
expression
microarray
console
7 days ago by
Mohammad
• 0
0
votes
6
replies
342
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
9 days ago by
hasani.iut6
▴ 60
1
vote
2
replies
267
views
DEgs RNAseq
RNAseq
9 days ago by
Juan
• 0
0
votes
0
replies
178
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
7 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
246
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 9 days ago by
Fabio Marroni
★ 3.0k • written 10 days ago by
1362321710
• 0
1
vote
1
reply
232
views
DownsampleSam
picard
DownsampleSam
updated 10 days ago by
Pierre Lindenbaum
154k • written 10 days ago by
mathalfilip
• 0
0
votes
1
reply
240
views
Error while running Megahit
Megahit
updated 10 days ago by
Mensur Dlakic
★ 23k • written 11 days ago by
abhiramiabhirami9072
• 0
2
votes
5
replies
418
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
8 days ago by
DanielEB_fisk
▴ 10
0
votes
0
replies
197
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
11 days ago by
dima
• 0
1
vote
0
replies
259
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
11 days ago by
abbas89
▴ 10
0
votes
1
reply
767
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
updated 7 days ago by
Joe
21k • written 11 days ago by
Aatif Hashmi
• 0
0
votes
1
reply
304
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2
RNA-seq
DGEA
updated 11 days ago by
Vincent Laufer
★ 2.9k • written 11 days ago by
Sara
▴ 10
1
vote
2
replies
271
views
Abyss taking a Long time to run
abyss
assembly
genome
fastq
11 days ago by
Maliha
▴ 20
0
votes
2
replies
296
views
Import or read Snapgene .dna files into R
R
.dna
snapgene
11 days ago by
eggrandio
▴ 40
4
votes
4
replies
360
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 8 days ago by
Joe
21k • written 12 days ago by
antoine.fauchois92
▴ 20
0
votes
0
replies
162
views
BEAST Divergence time Analysis
time
BEAST
BEAUti
divergence
12 days ago by
ahmadjoyyia
▴ 10
0
votes
0
replies
183
views
Differential Gene Expression analysis in heterogeneous tissues
RNA-seq
deseq2
updated 12 days ago by
Ram
39k • written 12 days ago by
txema.heredia
▴ 70
1
vote
1
reply
236
views
Variant Annotation
Variant-Annotation
VCF
R
updated 11 days ago by
Ram
39k • written 12 days ago by
Chethana
• 0
0
votes
2
replies
301
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
23 hours ago by
zhangdengwei
▴ 190
0
votes
1
reply
208
views
Finding Kinetic Parameters from Western Blot images
image-processing
western-blot
updated 11 days ago by
Ram
39k • written 12 days ago by
Vijeth
• 0
0
votes
0
replies
165
views
Chipseq data peak calling issue
ChIP-seq
RNA
sequencing
updated 7 days ago by
Ram
39k • written 12 days ago by
Adyasha
• 0
0
votes
0
replies
146
views
I want to set the null hypothesis for the test of genetic correlation to rg=1.
correlation
LDSC
genetic
12 days ago by
Apprentice
▴ 140
0
votes
2
replies
275
views
About inconsistent cell counts per samples obtained in small nuclear RNAseq data.
Seurat
QC
Single-Cell
11 days ago by
bk11
▴ 70
0
votes
1
reply
208
views
Identifying Mutation Frequency Changes in MSAs over time?
Mutation
Fasta
MSA
MutationRate
RNA-Seq
updated 12 days ago by
Vincent Laufer
★ 2.9k • written 12 days ago by
Saran
▴ 20
1
vote
1
reply
173
views
Import Pymol into Python Script
Pymol
python
updated 12 days ago by
Wayne
★ 1.8k • written 12 days ago by
jdrohan
• 0
1
vote
1
reply
155
views
making metadata file for differential gene expression analysis
RNAseq
updated 13 days ago by
Basti
★ 1.6k • written 13 days ago by
Sara
▴ 220
1
vote
2
replies
228
views
Create clustered bar chart in R
R
ggplot
visualization
12 days ago by
Prangan
▴ 20
0
votes
0
replies
113
views
Picard's CollectGcBiasMetrics gc-bias plot- help with interpretation
picard
gc-bias
wes
13 days ago by
bompipi95
▴ 120
0
votes
2
replies
197
views
Repbase database and transposon sequence
TE
TSD
TIRs
Tpase
12 days ago by
manaswiniparija3
▴ 10
0
votes
4
replies
289
views
How do I add row names to pheatmap() when I am using a pre-normalized matrix?
pheatmap
heatmap
rna-seq
updated 12 days ago by
Trivas
★ 1.2k • written 13 days ago by
mgranada3
• 0
566 results • Page
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ChatGPT optimized for bioinformatics questions
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Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
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Recent Replies
Comment: Which method is the best for using in "dba.count" in Diffbind R package
by
Rory Stark
★ 1.7k
If you are calling `dba.normalize()` directly, it must be called *after* calling `dba.count()`. `dba.count()` will apply the default normal…
Comment: switching from illumination to NEB prep kits
by
GenoMax
129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
Zhichao
• 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2
by
ATpoint
72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts
by
ATpoint
72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
ATpoint
72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
Thanks a lot, it works
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
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