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121,507 results • Page
1 of 2431
Sort: Rank
Rank
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Votes
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1
vote
2
replies
664
views
Running trajectory and velocity analysis with multiple samples
seurat
velocity
loom
trajectory
written 15 months ago by
gogeni5529
▴ 70
0
votes
3
replies
173
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 1 hour ago by
Gordon Smyth
★ 8.2k • written 19 hours ago by
Guillermo
• 0
0
votes
0
replies
47
views
NMR modelling using xplor-NIH
peptide
xplor-NIH
NMR
9 hours ago by
npk107
• 0
1
vote
3
replies
121
views
PCA interpretation
chip
seq
PCA
updated 9 hours ago by
rfran010
★ 1.6k • written 12 hours ago by
Irving
• 0
0
votes
2
replies
106
views
UCSC genome browser negative strand positions
Genomic
Data
Browser
UCSC
Visualization
Genome
updated 7 hours ago by
rfran010
★ 1.6k • written 17 hours ago by
ijarne
▴ 20
840
votes
170
replies
181k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
0
replies
64
views
News:
course: Reproducibility in Bioinformatics - Only 2 seats remain!
Singularity
Git
Reproducibility
Docker
Snakemake
21 hours ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
61
views
Annotate phylogenetic trees with bars or strips
otu
phylogenetics
R
taxonomy
metabarcoding
22 hours ago by
Luca Arbore
▴ 10
2
votes
2
replies
250
views
Identifying Long Reads Spanning Chromosomal Breakpoints
ONT
samtools
Whole-Genome
updated 1 day ago by
trausch
★ 2.0k • written 2 days ago by
Noah
▴ 10
0
votes
1
reply
145
views
PAML output
PAML
Codeml
Selection
updated 22 hours ago by
manaswwm
▴ 570 • written 1 day ago by
Morjina
• 0
0
votes
0
replies
119
views
how to produce your own Nx plot
R
contiguity
plot
Nx
1 day ago by
Matteo Ungaro
▴ 120
1
vote
2
replies
204
views
Interpreting inconsistency between BLAST hits and phylogenetic clustering i
tree
phylogenetic
blast
19 hours ago by
triplee0305
▴ 20
0
votes
0
replies
87
views
News:
Online course - Environmental Metagenomics - 13-17 October
Illumina
MAGs
Nanopore
Metagenomics
1 day ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
196
views
Deg Difference in Deseq2
Deg
updated 1 day ago by
swbarnes2
15k • written 1 day ago by
j.k.owaresat
• 0
0
votes
0
replies
137
views
No gene_trans_map file in CD-HIT-EST output
cd-hit-est
Trinity
RNAseq
Trinotate
updated 1 day ago by
GenoMax
152k • written 1 day ago by
ofarinas621
• 0
0
votes
3
replies
236
views
MultiQC report - unique reads from sequence counts
fastQC
unique
reads
multiQC
20 hours ago by
Rozita
▴ 40
2
votes
3
replies
224
views
NCBI Reference Genomes
genomes
ncbi
updated 1 day ago by
GenoMax
152k • written 1 day ago by
anna
▴ 70
0
votes
0
replies
117
views
GATK HaplotypeCaller missed variants in amplicon gene panel data
amplicon
gene_panel
haplotypecaller
variant_calling
gatk
1 day ago by
Sofya
• 0
0
votes
0
replies
189
views
Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger multi with Combined Human-Mouse Reference
gem_classification
10x
cellranger_multi
combined_human-mouse_reference
1 day ago by
tlallihuacan
• 0
0
votes
0
replies
97
views
Extracting logR and Baf files genome studio
Genomestudio
1 day ago by
1769mkc
★ 1.3k
0
votes
1
reply
272
views
Statistical analysis in a metagenomics study to validate biological differences
Metagenomics
analysis
updated 1 day ago by
chen
★ 2.5k • written 5 days ago by
Chijioke
• 0
1
vote
2
replies
466
views
Assembly issues
adapters
Assembly
Spades
updated 1 day ago by
chen
★ 2.5k • written 29 days ago by
anna
• 0
0
votes
5
replies
484
views
Trouble removing adapters from sequences using cutadapt
removal
cutadapt
adapter
primer
updated 1 day ago by
chen
★ 2.5k • written 7 days ago by
k.lagan
• 0
0
votes
5
replies
1.8k
views
Fastp
fastp
updated 2 days ago by
chen
★ 2.5k • written 3.2 years ago by
nishimalhotra2612
▴ 50
5
votes
10
replies
595
views
Need help using ExpansionHunter
ExpansionHunter
3 hours ago by
brianhill_nc
• 0
0
votes
1
reply
162
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 22 hours ago by
manaswwm
▴ 570 • written 2 days ago by
decorus
• 0
0
votes
0
replies
148
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
2 days ago by
Cassandra
• 0
0
votes
0
replies
177
views
Comparing and plotting multinomial elastic net performance
ROC
elasticnet
plotting
glmnet
machinelearning
2 days ago by
bioinfo
• 0
2
votes
3
replies
303
views
How to add gene lable on GSEA plot
gseaplot
R
updated 1 day ago by
yura.grabovska
▴ 780 • written 2 days ago by
Emy Alade
▴ 20
0
votes
0
replies
176
views
Adding New Samples to Existing VCF Files graphtyper2
graphtyper2
existing_vcf
add_new_samples
2 days ago by
upadhyay.maulik
• 0
2
votes
5
replies
366
views
Seurat dims and QC questions
dims
updated 2 days ago by
1769mkc
★ 1.3k • written 3 days ago by
reddyornah
• 0
1
vote
1
reply
233
views
Duplication rate as reported by fastp.
fastp
duplication
RNA-seq
updated 3 days ago by
GenoMax
152k • written 3 days ago by
Anjan
▴ 840
0
votes
2
replies
495
views
Is it appropriate to include singleton reads with paired-end datasets for low-coverage Anaplasma marginale comparative genome analysis?
assembly
analysis
coverage
genome
singletons
comparative
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
ashiqullah024
• 0
0
votes
7
replies
405
views
Ligand-Receptor analysis using LIANA - question about specificity
scRNA-seq
communication
cell-cell
updated 15 hours ago by
m.sharghi
• 0 • written 3 days ago by
abedkurdi10
▴ 190
0
votes
0
replies
183
views
ComBat for Multiple Batch Effects in Methylation Data (Chip, Row, Plate)
ComBat
methylation
EPIC
batch-correction
3 days ago by
Eliveri
▴ 350
0
votes
1
reply
214
views
Using a Seurat object to create a cellchat object
cellchat
1 day ago by
m.sharghi
• 0
0
votes
0
replies
185
views
WGCNA - High R2 and Mean connectivity at low soft power
WGCNA
3 days ago by
Leonard Barnabas
• 0
0
votes
0
replies
160
views
How do I combine or integrate my VDJ data for TCR and BCR with seurat object?
VDJ
scRepertoire
Seurat
updated 3 days ago by
GenoMax
152k • written 3 days ago by
Jaber
▴ 30
0
votes
2
replies
348
views
DGE analysis in Seurat using paired samples per donor ?
paired
seurat
dge
sample
17 hours ago by
Picasa
▴ 680
2
votes
3
replies
425
views
RNA-seq: TPM batch effect correction
TPM
Combat
RNA-seq
updated 5 days ago by
rfran010
★ 1.6k • written 6 days ago by
Samuel
▴ 10
1
vote
3
replies
353
views
Error running pbrun fq2bam: No space left on device
disk
space
updated 4 days ago by
DBScan
▴ 490 • written 6 days ago by
Ritu
• 0
2
votes
3
replies
1.8k
views
How to find the annotation file for GPL16956 platform of Arraystar human lncRNA microarray V3 (Probe Name Version)?
annotation
lncRNA
microarray
probe
updated 4 days ago by
GenoMax
152k • written 5.1 years ago by
daphneolivia39
▴ 20
1
vote
5
replies
390
views
Statistics for bins
data
shotgun
updated 4 days ago by
GenoMax
152k • written 4 days ago by
shevch2009
▴ 20
5
votes
4
replies
439
views
twist exome panel analysis
twist
exome
updated 4 days ago by
GenoMax
152k • written 7 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
232
views
Run hifiasm without error correction module?
hifiasm
assembly
wgs
nanopore
genomics
updated 4 days ago by
shelkmike
★ 1.6k • written 5 days ago by
Mark
▴ 60
1
vote
1
reply
257
views
PhageTerm Galaxy
error
phageterm
genomics
updated 5 days ago by
GenoMax
152k • written 5 days ago by
NIkita
• 0
1
vote
1
reply
258
views
Demultiplexing of snAtcSeq data using demuxlet gives an empty output
genotype
demuxlet
scatacseq
demultiplexing
updated 5 days ago by
GenoMax
152k • written 5 days ago by
Bioiris
▴ 10
0
votes
1
reply
519
views
PbJelly Resume
Gap-filling
PacBio
PbJelly
written 12 months ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
205
views
How do I figure out which chain a ligand is bound to using rcsb-api?
rcsb
updated 5 days ago by
GenoMax
152k • written 6 days ago by
Priyal
▴ 10
1
vote
2
replies
384
views
Deseq2
PyDeseq2
Deseq2
updated 6 days ago by
GenoMax
152k • written 6 days ago by
sk_24
▴ 10
121,507 results • Page
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Comment: Need help using ExpansionHunter
by
brianhill_nc
• 0
Thanks, I will work on that more soon. Someone said that you could simply count CAG repeats on the genome browser of Nebula from certain …
Comment: UCSC genome browser negative strand positions
by
rfran010
★ 1.6k
Would this be related to some function that takes the "end" as the start for negative strand features? E.g. Exon1: chr1 100 500 E…
Answer: Weird p-value distribution on edgeR results
by
Gordon Smyth
★ 8.2k
You say that PCA principal components were between -100 and 100. I don't know how you have constructed the PCA plot but, if you have used e…
Comment: What's the difference of FPKM generated by htseq and stringtie?
by
barbara.dobrin
• 0
Hi, do you know if StringTie computes effective feature lengths and uses those in the denominator when it computes FPKM, or if it uses the …
Comment: PCA interpretation
by
rfran010
★ 1.6k
Assuming this is deepTools, I recommend reviewing the documentation and choosing one of the two indicated options: Named Arguments …
Comment: PCA interpretation
by
Irving
• 0
I used the following script: # BAM files R1="DMSO_H1_noduplicates_sorted.bam" R2="DMSO_H2_noduplicates_sorted.bam" R4="TPL_H1_noduplicates…
Comment: Weird p-value distribution on edgeR results
by
rfran010
★ 1.6k
If you're confident in the experimental design and analysis, then this would indicate two sample with few DEGs? For example, I have an indu…
Comment: PCA interpretation
by
jared.andrews07
★ 19k
How did you do this PCA and make these plots? The axes labels for variation make no sense (and thus I suspect they were swapped).
Answer: Weird p-value distribution on edgeR results
by
LChart
5.0k
> Even after its removal, the weird p-value distribution didn't change. Did you re-run PCA after its removal to look for more outliers? Ou…
Comment: Ligand-Receptor analysis using LIANA - question about specificity
by
m.sharghi
• 0
Nice, Do you think we can discuss more on this?
Comment: UCSC genome browser negative strand positions
by
Pierre Lindenbaum
166k
> hen make a transformation where we pick the mutation and then we transform their coordinates to the coordinates of the exons that is occu…
Comment: How to run delly with multi-threading mode?
by
thomas.heigl.ibk
• 0
thanks. then i don't get it. it is still running. gridss, lumpy and manta ran normally though. maybe i will exclude delly if it still run…
Comment: DGE analysis in Seurat using paired samples per donor ?
by
Picasa
▴ 680
I did already a pseudobulk approach. I would like now to compare with single cell specific methods (like MAST)
Comment: Interpreting inconsistency between BLAST hits and phylogenetic clustering i
by
triplee0305
▴ 20
Thank you for the response — your points make a lot of sense! Yes, I did trim the alignment using **trimAl** with the `-automated1` option…
Comment: MultiQC report - unique reads from sequence counts
by
Rozita
▴ 40
Thank you. I meant a clean up with beads, which I definitely understand is a wet-lab step. I meant that another round of beads clean-up wou…
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