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869 results • Page
4 of 18
Sort: Rank
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Votes
Replies
0
votes
0
replies
120
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
7 days ago by
Christopher
• 0
4
votes
1
reply
245
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 6 days ago by
zx8754
11k • written 8 days ago by
Jautis
▴ 560
2
votes
2
replies
335
views
Association study using SNP data
Association
Allele
Parentage
SNP
7 days ago by
drajangirija
• 0
0
votes
0
replies
113
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
7 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
122
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
7 days ago by
DGTool
• 0
2
votes
3
replies
313
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 3 days ago by
bk11
★ 2.4k • written 7 days ago by
Yoosef
▴ 60
0
votes
1
reply
592
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 7 days ago by
GenoMax
142k • written 8 days ago by
tulip
• 0
3
votes
4
replies
430
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 6 days ago by
Gordon Smyth
★ 7.1k • written 9 days ago by
SHN
▴ 40
4
votes
2
replies
269
views
GRCh38.gmap file
gnomix
gmap
8 days ago by
lorena9132
▴ 10
2
votes
3
replies
828
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 8 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
1
reply
265
views
creating batch colum for batch correction
batch-correction
combat
6 days ago by
Expert
▴ 10
1
vote
4
replies
370
views
Segmentation error while using a tool
smalt
updated 8 days ago by
Mensur Dlakic
★ 27k • written 9 days ago by
Ruqaiya
• 0
0
votes
1
reply
228
views
Help with DGEList function
DGEList
R
updated 7 days ago by
marco.barr
▴ 100 • written 8 days ago by
Natali
• 0
0
votes
0
replies
158
views
Homer motif analysis
Homer
8 days ago by
daffodil
▴ 10
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
7 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
315
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 9 days ago by
chrchang523
10k • written 12 days ago by
8armed
▴ 10
0
votes
5
replies
362
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 9 days ago by
chrchang523
10k • written 9 days ago by
curious
▴ 750
0
votes
1
reply
221
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 8 days ago by
Ram
43k • written 9 days ago by
Rob
▴ 170
0
votes
2
replies
257
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 2 days ago by
GenoMax
142k • written 9 days ago by
Ximena
• 0
0
votes
1
reply
204
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 8 days ago by
Ram
43k • written 9 days ago by
Valentina
• 0
0
votes
6
replies
448
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 9 days ago by
swbarnes2
14k • written 9 days ago by
Erina
• 0
0
votes
2
replies
240
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
6 days ago by
kalavattam
▴ 190
1
vote
3
replies
301
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
7 days ago by
Lada
▴ 30
1
vote
0
replies
152
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 6 days ago by
zx8754
11k • written 9 days ago by
Emilie
▴ 10
0
votes
0
replies
142
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
9 days ago by
Javier
• 0
0
votes
2
replies
270
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 hours ago by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
yahn
• 0
0
votes
0
replies
134
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
9 days ago by
mikemakaveli1
• 0
2
votes
2
replies
232
views
Raw counts using stringtie
stringtie
RNA-seq
updated 9 days ago by
GenoMax
142k • written 9 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
134
views
Modify plot R mtDNA indel
plot
mtDNA
R
9 days ago by
marco.barr
▴ 100
0
votes
0
replies
324
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
9 days ago by
NorbertK
▴ 10
4
votes
2
replies
248
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 8 days ago by
Ram
43k • written 9 days ago by
carolofharvest
▴ 40
13
votes
14
replies
841
views
High Malat-1 expression in single cell data
single-cell
updated 4 days ago by
t.montserrat.ayuso
▴ 40 • written 13 days ago by
carolofharvest
▴ 40
0
votes
2
replies
262
views
Downloading older version of a tool
Alignment
tools
9 days ago by
Ruqaiya
• 0
0
votes
0
replies
153
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
9 days ago by
rustykb
▴ 20
1
vote
1
reply
196
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 8 days ago by
Ram
43k • written 9 days ago by
adi.gershon1
• 0
3
votes
5
replies
302
views
Generating mpileup file using samtools
mpileup
samtools
updated 9 days ago by
Joe
21k • written 9 days ago by
Ruqaiya
• 0
0
votes
5
replies
384
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 9 days ago by
b.contreras.moreira
▴ 180 • written 10 days ago by
JH
• 0
1
vote
3
replies
295
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 9 days ago by
ATpoint
82k • written 10 days ago by
Qi
• 0
0
votes
0
replies
142
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
9 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
302
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 9 days ago by
dthorbur
★ 1.9k • written 9 days ago by
Vijith
▴ 30
0
votes
0
replies
157
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
10 days ago by
Jeyong
• 0
0
votes
2
replies
735
views
homer not configured properly
Homer
makeTagDirectory
updated 10 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
1
vote
3
replies
286
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 10 days ago by
Alex Reynolds
35k • written 10 days ago by
SJP
• 0
0
votes
0
replies
141
views
Empty table plot using plotGseaTable()
FGSEA
9 days ago by
Chris
▴ 280
0
votes
1
reply
198
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 10 days ago by
anovak
▴ 120 • written 10 days ago by
Hang
• 0
1
vote
3
replies
249
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 10 days ago by
jared.andrews07
★ 16k • written 10 days ago by
yvonneh
▴ 10
3
votes
5
replies
352
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
9 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 10 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
213
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
10 days ago by
dtnondorf
• 0
3
votes
8
replies
630
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 6 days ago by
Chris Dean
▴ 410 • written 10 days ago by
sovrappensiero
▴ 100
869 results • Page
4 of 18
Recent Votes
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
Comment: automatic clustering annotation using python
automatic clustering annotation using python
Answer: How to compute TPM normalized values for TCGA miRNA data?
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
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Answer: Generating .bed file and .map file for polyploid vcf file through plink
by
chrchang523
10k
Why do you think ADMIXTURE supports polyploid input? (Note that this is an answer, not a comment.)
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
Comment: Extracting mutation status from MAF files - TCGA
by
Zhenyu Zhang
★ 1.2k
you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38
by
Zhenyu Zhang
★ 1.2k
Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
Answer: Nomalization - TCGA, RNA-seq and Microarray
by
Zhenyu Zhang
★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
by
ATpoint
82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
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Pine
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This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
Answer: Tissue-specific DEG analysis with DEseq2
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arctic
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Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
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by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
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There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
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