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174 results • Page
1 of 4
Sort: Votes
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Views
Votes
Replies
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
6 days ago by
Kevin Blighe
87k
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 1 day ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
37
votes
24
replies
1.7k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 day ago by
i.sudbery
19k • written 3 days ago by
noodle
▴ 580
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 4 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 6 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 5 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
8
votes
8
replies
615
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
Aaliya
▴ 10
8
votes
16
replies
914
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 4 days ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 5 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
5
votes
6
replies
390
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 17 hours ago by
me
▴ 760 • written 1 day ago by
Mariana
▴ 40
5
votes
3
replies
202
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 1 day ago by
Lluís R.
★ 1.2k • written 1 day ago by
이민경[학생](대학원 융합의과학과)
• 0
5
votes
16
replies
627
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
2 days ago by
Ruqaiya
• 0
4
votes
0
replies
118
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
1 day ago by
Biostar
2.7k
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 1 day ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
4
votes
4
replies
422
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 3 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
Ming Tommy Tang
★ 3.9k
4
votes
7
replies
539
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
1 day ago by
e.r.zakiev
▴ 200
4
votes
5
replies
261
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 1 day ago by
dsull
★ 5.9k • written 1 day ago by
Kazo
▴ 10
4
votes
7
replies
662
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 4 days ago by
dsull
★ 5.9k • written 8 days ago by
qudrat.nii
▴ 10
4
votes
7
replies
479
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 6 days ago by
dsull
★ 5.9k • written 7 days ago by
VITALA
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
1 day ago by
anna
▴ 20
4
votes
3
replies
340
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 3 days ago by
Arup Ghosh
3.2k • written 4 days ago by
chaco001
▴ 40
4
votes
2
replies
386
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 5 days ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
4
votes
8
replies
620
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 4 days ago by
Alex Reynolds
35k • written 5 days ago by
J
▴ 10
4
votes
2
replies
279
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
1 day ago by
pairedttest
▴ 10
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 5 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 4 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
3
votes
2
replies
276
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
vanbelj
▴ 40
3
votes
7
replies
264
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
1 day ago by
salias
• 0
3
votes
3
replies
293
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 5 days ago by
swbarnes2
14k • written 5 days ago by
M
• 0
3
votes
3
replies
270
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 1 day ago by
noodle
▴ 580 • written 2 days ago by
WUSCHEL
▴ 750
3
votes
0
replies
195
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 4 days ago by
Ram
43k • written 5 days ago by
Claire Watson
▴ 60
3
votes
4
replies
340
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
5 days ago by
QX
• 0
3
votes
2
replies
317
views
Extract protein sequence
fasta
alignment
blast
15 hours ago by
anna
▴ 20
3
votes
3
replies
288
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 4 days ago by
GenoMax
141k • written 5 days ago by
sapuizait
▴ 10
3
votes
2
replies
322
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 4 days ago by
dsull
★ 5.9k • written 5 days ago by
Aaliya
▴ 10
3
votes
9
replies
483
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 6 days ago by
Istvan Albert
100k • written 8 days ago by
Κοσμάς
• 0
2
votes
11
replies
862
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 2 days ago by
jkbonfield
★ 1.2k • written 13 days ago by
me
• 0
2
votes
2
replies
282
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 6 days ago by
Ram
43k • written 7 days ago by
v.berriosfarias
▴ 140
2
votes
1
reply
229
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 6 days ago by
Adrian Altenhoff
★ 1.1k • written 6 days ago by
hemantcnaik
• 0
2
votes
5
replies
325
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
5 days ago by
Lada
▴ 30
2
votes
5
replies
336
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
2 days ago by
analyst
▴ 30
2
votes
2
replies
134
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Sudip
• 0
2
votes
4
replies
266
views
from row count to tpm
tpm
row-count
normalization
updated 18 hours ago by
Ram
43k • written 8 days ago by
michelafrancesconi9
▴ 20
2
votes
5
replies
919
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 1 day ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
2
votes
5
replies
436
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
2 days ago by
ashaneev07
▴ 20
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 1 day ago by
Medhat
9.7k • written 24 months ago by
Vitor1
▴ 120
2
votes
2
replies
186
views
PDB related issue
rcsb
pdb
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
Nafi
• 0
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 5 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 6 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
3
replies
345
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 4 days ago by
dsull
★ 5.9k • written 21 days ago by
javanokendo
▴ 60
174 results • Page
1 of 4
Recent Votes
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Comment: Programmatically retrieving positions of protein active site residues
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Comment: p-value in CIBERSORT
by
michelafrancesconi9
▴ 20
Thank you so much!!
Comment: DESeq2 processing problems
by
ATpoint
82k
https://support.bioconductor.org/p/9158036/#9158037 > ...make your question reproducible by putting data and code You're free to ignore a…
Comment: POSSUM not working due to incompatible pssm file
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: after selecting specific GO terms to plot, cneplot is not showing any color for
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Telescope issue
by
GenoMax
141k
Looks like there is a tab missing between the sequence and the quality string.
Comment: Post-imputation plot
by
LChart
3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue
by
eleven11
• 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
Aspire
▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue
by
GenoMax
141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
Comment: KEGG Pathways
by
Ram
43k
Give us as much detail as you can. What error does it give you?
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 320
- `p.adjust()` is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, …
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