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116,760 results • Page
4 of 2336
Sort: Rank
Rank
Views
Votes
Replies
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 6 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
481
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
6 days ago by
ashaneev07
▴ 20
0
votes
1
reply
172
views
Downloading full alignments from Pfam
pfam
updated 6 days ago by
GenoMax
142k • written 6 days ago by
bef1
• 0
0
votes
1
reply
753
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 6 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
299
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 5 days ago by
i.sudbery
19k • written 8 days ago by
vanbelj
▴ 40
0
votes
0
replies
123
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 5 days ago by
dariober
14k • written 7 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
306
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 6 days ago by
ATpoint
82k • written 7 days ago by
Francesco
▴ 10
0
votes
0
replies
140
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
7 days ago by
tnminh89
▴ 10
0
votes
0
replies
146
views
Filter low express genes in microarray data
microarray
7 days ago by
Chris
▴ 260
0
votes
1
reply
336
views
absolute path for symbolic links in Snakefile
Snakemake
updated 7 days ago by
Jesse
▴ 740 • written 15 days ago by
yifangt86
▴ 60
0
votes
2
replies
359
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 7 days ago by
Jesse
▴ 740 • written 10 days ago by
Broccoli
• 0
4
votes
3
replies
370
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 7 days ago by
Arup Ghosh
3.2k • written 8 days ago by
chaco001
▴ 40
1
vote
3
replies
396
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 6 days ago by
Mensur Dlakic
★ 27k • written 8 days ago by
O.rka
▴ 710
0
votes
2
replies
261
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
7 days ago by
Guille
• 0
4
votes
2
replies
305
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
5 days ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 8 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
571
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
8 days ago by
biocellbio
• 0
4
votes
8
replies
666
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 8 days ago by
Alex Reynolds
35k • written 9 days ago by
J
▴ 10
4
votes
7
replies
712
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 8 days ago by
dsull
★ 6.0k • written 12 days ago by
qudrat.nii
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 8 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
3
votes
2
replies
334
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 8 days ago by
dsull
★ 6.0k • written 9 days ago by
Aaliya
▴ 10
3
votes
0
replies
212
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 8 days ago by
Ram
43k • written 8 days ago by
Claire Watson
▴ 60
0
votes
2
replies
290
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 8 days ago by
Ram
43k • written 9 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
206
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
8 days ago by
HarperReed
• 0
3
votes
3
replies
313
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 8 days ago by
GenoMax
142k • written 8 days ago by
sapuizait
▴ 10
1
vote
0
replies
161
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
9 days ago by
KABILAN
▴ 70
0
votes
0
replies
178
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 8 days ago by
Ram
43k • written 9 days ago by
SineWave
• 0
0
votes
0
replies
173
views
RNA-seq: full length gene
RNA-seq
updated 8 days ago by
Ram
43k • written 9 days ago by
Nargis
• 0
1
vote
7
replies
507
views
gvcf joint calling
WES
GATK
VCF
gVCF
6 days ago by
zihanss
• 0
0
votes
0
replies
157
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
9 days ago by
turcoa1
• 0
3
votes
3
replies
325
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 9 days ago by
swbarnes2
14k • written 9 days ago by
M
• 0
0
votes
0
replies
167
views
Designing single-stable RNA molecules
structure
RNA
9 days ago by
Edna
• 0
0
votes
0
replies
179
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
9 days ago by
simplitia
▴ 130
1
vote
1
reply
233
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 9 days ago by
ATpoint
82k • written 9 days ago by
AaronJaime
• 0
0
votes
2
replies
303
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 9 days ago by
GenoMax
142k • written 9 days ago by
Begonia_pavonina
▴ 150
0
votes
3
replies
402
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
4 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
345
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
7 days ago by
Francesco
▴ 10
1
vote
7
replies
517
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 5 days ago by
bk11
★ 2.4k • written 9 days ago by
starswillfade
▴ 10
0
votes
0
replies
168
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 9 days ago by
Ram
43k • written 9 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
164
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
9 days ago by
Emily
▴ 10
1
vote
0
replies
176
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
9 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
160
views
how to read graph_test output of monocle 3
monocle3
9 days ago by
synat.keam
▴ 100
1
vote
0
replies
211
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
9 days ago by
Assaf
▴ 10
0
votes
1
reply
511
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 9 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
3
votes
4
replies
379
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
9 days ago by
QX
• 0
2
votes
1
reply
250
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 9 days ago by
Adrian Altenhoff
★ 1.1k • written 10 days ago by
hemantcnaik
• 0
0
votes
0
replies
159
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
9 days ago by
Aspire
▴ 330
2
votes
5
replies
384
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
6 days ago by
analyst
▴ 30
0
votes
3
replies
325
views
Highest variable features in single cell data
single-cell
updated 8 days ago by
bk11
★ 2.4k • written 10 days ago by
carolofharvest
▴ 30
0
votes
1
reply
230
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 10 days ago by
Scooter
▴ 280 • written 10 days ago by
Akash D
▴ 40
116,760 results • Page
4 of 2336
Recent Votes
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
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Comment: The GDC Legacy Archive is retiring soon.
by
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If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
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These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
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> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
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Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
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Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
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Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
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Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
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I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
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Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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This the tool still problematic?
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Thank you for the advice, i'll keep that in mind.
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I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
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Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
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Thanujay S
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Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
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