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681 results • Page
7 of 14
Sort: Votes
Rank
Views
Votes
Replies
1
vote
7
replies
563
views
Question regarding WGCNA
WGCNA
Network-construction
9 days ago by
deepak
• 0
1
vote
1
reply
216
views
Failed kmer content
kmer
illumina
ngs
updated 25 days ago by
Ram
43k • written 26 days ago by
Kasturi
• 0
1
vote
3
replies
274
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 2 days ago by
GenoMax
142k • written 5 days ago by
ohtang7
▴ 40
1
vote
1
reply
189
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
18 days ago by
heelpPlease
• 0
1
vote
3
replies
343
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
13 days ago by
Lada
▴ 30
1
vote
5
replies
816
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 29 days ago by
BioinfGuru
★ 1.7k • written 4 weeks ago by
rrehimi
• 0
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
24 days ago by
DKA
▴ 40
1
vote
3
replies
279
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 2 days ago by
Ram
43k • written 3 days ago by
kuttibiotech2009
▴ 30
1
vote
1
reply
200
views
Super ehancers
enhancers
updated 16 days ago by
jared.andrews07
★ 16k • written 16 days ago by
Oburah
• 0
1
vote
1
reply
250
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 25 days ago by
Istvan Albert
100k • written 26 days ago by
Abeer
• 0
1
vote
4
replies
421
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 8 days ago by
GenoMax
142k • written 4 weeks ago by
aniigodwinn
• 0
1
vote
0
replies
161
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 13 days ago by
zx8754
11k • written 15 days ago by
Emilie
▴ 10
1
vote
3
replies
340
views
some error in building kraken2 database
metagenome
kraken2
25 days ago by
Art1ess
• 0
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 10 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
1
vote
1
reply
170
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 16 days ago by
Ram
43k • written 17 days ago by
marco.barr
▴ 130
1
vote
4
replies
493
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 25 days ago by
atowns21
• 0 • written 6 months ago by
ara
• 0
1
vote
2
replies
363
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 5 days ago by
Ram
43k • written 6 days ago by
t.fortunato.asquini
• 0
1
vote
5
replies
502
views
How should I make kallisto indexes?
kallisto
updated 19 days ago by
dsull
★ 6.0k • written 4 weeks ago by
bioinfo
▴ 150
1
vote
2
replies
282
views
permutation test in edgeR
rna-seq
edgeR
updated 27 days ago by
Gordon Smyth
★ 7.2k • written 5 weeks ago by
Netanel
• 0
1
vote
2
replies
266
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 12 days ago by
zx8754
11k • written 12 days ago by
snajafy
• 0
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
14 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
7
replies
617
views
gvcf joint calling
WES
GATK
VCF
gVCF
21 days ago by
zihanss
• 0
1
vote
3
replies
309
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
25 days ago by
WouterDeCoster
47k
1
vote
1
reply
249
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
3 days ago by
ramiro.barrantes
• 0
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
4
replies
451
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
19 days ago by
hagl
▴ 10
1
vote
0
replies
255
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
23 days ago by
Assaf
▴ 10
1
vote
8
replies
454
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 1 day ago by
Alex Reynolds
35k • written 5 days ago by
ntsopoul
▴ 60
1
vote
5
replies
326
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 1 day ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
4 days ago by
Lukas
• 0
0
votes
5
replies
445
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 16 days ago by
b.contreras.moreira
▴ 200 • written 16 days ago by
JH
• 0
0
votes
2
replies
234
views
Result of running of p3_in.pl
primer3
updated 26 days ago by
GenoMax
142k • written 27 days ago by
nasri
• 0
0
votes
1
reply
305
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 29 days ago by
GenoMax
142k • written 29 days ago by
bioyas
▴ 10
0
votes
2
replies
754
views
homer not configured properly
Homer
makeTagDirectory
updated 16 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
3 days ago by
jway
• 0
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 5 days ago by
GenoMax
142k • written 5 days ago by
cedric.blais
• 0
0
votes
3
replies
197
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 11 days ago by
GenoMax
142k • written 11 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
310
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
0
votes
5
replies
6.0k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 28 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
0
replies
132
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
2 days ago by
Jsarria.EEAD
• 0
0
votes
0
replies
124
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 16 days ago by
Ram
43k • written 17 days ago by
carlopecoraro2
★ 2.5k
0
votes
9
replies
606
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
3 days ago by
Arton
▴ 10
0
votes
0
replies
157
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 27 days ago by
Carlo Yague
8.7k • written 27 days ago by
Atul K.
• 0
0
votes
0
replies
131
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
13 days ago by
DGTool
▴ 20
0
votes
0
replies
284
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 26 days ago by
Ram
43k • written 15 months ago by
Pine
▴ 20
0
votes
2
replies
179
views
How/where can I get fungal mitogenome data for analysis?
fungal
mitogenome
updated 10 days ago by
GenoMax
142k • written 10 days ago by
madders73
• 0
0
votes
0
replies
122
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
17 days ago by
VITALA
• 0
0
votes
1
reply
197
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 6 days ago by
chrchang523
10k • written 11 days ago by
analyst
▴ 50
0
votes
0
replies
71
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 16 hours ago by
Pierre Lindenbaum
161k • written 16 hours ago by
Mohamed Samir
▴ 20
0
votes
2
replies
491
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 11 days ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
681 results • Page
7 of 14
Recent Votes
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
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▴ 260
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★ 6.0k
Recent Replies
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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