6/11/22:
- Fix bug that caused the cvar
fwr4_dna_ref
to have its rightmost base removed.
- Add cvars for leader variables.
5/9/22: Add ability to create enclone visual sessions from the command line. Please
see enclone visual.
5/8/22: enclone now runs under Windows, with some limitations, see
here.
3/31/22:
- Add lvars
jun_mat
and jun_sub
.
- Add option
NOGRAY
to turn off gray color in per-cell clonotype lines.
3/26/22: Add lvar jun_ins
, please see
enclone help lvars
.
3/15/22: Add DATASET
filter, please see
enclone help filter
.
3/14/22:
3/11/22:
- A major change to the clonotype joining algorithm, which joins based on sharing in the
heavy chain junction region, and which substantially increases clonotyping sensitivity. Please
see
enclone help how
. This change also
makes enclone about 30% slower.
- Delete the following genes from the human VDJ reference: IGHV4-30-2, IGKV1D-33, IGKV1D-37,
IGKV1D-39, IGKV2D-28. These are identical to other genes in the reference, except that the
reference provides a longer 5'-UTR in one case. We observe that clonotypes having one of these
genes often have heterogeneous assignments between the gene and its duplicate, and that's bad,
as it implies that assignment of genes to clonotypes in these cases is effectively random.
- Add lvars
allele
and allele_d
. Please see
enclone help lvars
.
3/4/22: Add ability to select functional groups by donor, see
enclone help display
.
3/3/22:
- Import a large set of data from iReceptor.
- Add grouping option
v_heavy_refname
.
- Add
PREPOST=x
to append /x
to PRE
entries.
- Allow multiple
META
arguments and allow each META
to be a
comma-separated list of filenames.
3/2/22:
- Add grouping options
cdr3_heavy_len
and cdr3_light_len
.
- Clonotypes within groups are now reverse sorted by cell count.
- Add
GROUP_CDR3
to only show groups containing the given CDR3 amino acid
sequence.
For all of the above, please see
enclone help display
.
- Add ability to plot by a categorical variable. Please see
enclone plots.
2/28/22: Add an argument BC_JOINT=filename
, which functions like
BC
, but uses only a single file. Please see
enclone help input
.
2/25/22:
-
For the
medium
and large
enclone installation
options, some published customer datasets are now included, from LIBRA-seq and for Kawasaki
disease, Wang et al. 2021 Nature Communications,
"Single-cell RNA sequencing of peripheral blood mononuclear cells from acute
Kawasaki disease patients".
- Change the default for
JOIN_CDR3_IDENT
from 80
to 85
.
2/18/22: Introducing enclone visual! This is alpha software for a
graphic user interface (GUI) for enclone, that is implemented initially for Macs.
Please see enclone visual.
2/16/22: Add new grouping options, please see
enclone help display
.
2/14/22:
- Two more changes to the clonotyping join algorithm, see
here.
- Add
SPLIT_PLOT_BY_DATASET
, see
enclone plots.
2/7/22: Remove some genes from the reference that were identical except for extension
on the 3' end.
2/4/22:
- Improve the correctness of V gene assignment. The changes comprise several technical changes
to the alignment code and the addition of one gene IGHV3-9 to the VDJ reference. About 2%
of cells are affected.
- Add lvars
vname_orig
and dref_max
.
1/26/22: Add ability to define variables as expressions involving other variables,
using an argument VAR_DEF=...
. Please see
variables
.
1/13/22: Make three small changes to BCR clonotyping:
- Change the default value for
MAX_SCORE
to 100000
.
- Fix bug that resulted in the constraint
cd ≤ 15
still being imposed.
- Allow joins with high score to pass so long as they have at least
15
shared
mutations. The parameter 15
is accessible as AUTO_SHARE
.
1/5/22:
- Several changes that improve clonotyping sensitivity and specificity. Details are
here and also reflected in
enclone help how
.
- Add an option
JOIN_BASIC=...
to use a much simpler clonotyping join criterion.
See enclone help how
.
12/27/21:
- Fix bug in computation of the cvars
vj_seq_nl
and
vj_aa_nl
. These were not correctly handling the case where there is an indel in the
leader sequence.
- Fix bug in computation of cvars
fwr3_dna
and fwr3_aa
. These were
not correctly handling the case where there was a deletion in the sequence before the CDR3 start.
12/24/21: Add filter option NMAX
to allow barcodes having more than four
contigs. Also, this is now turned on by NALL
and NALL_CELL
. This
does not affect default behavior.
12/13/21:
This version includes three changes that substantially improve clonotyping specificity. See
below and enclone help how
.
- Change clonotyping algorithm by rejecting joins where the number of differences in CDR3
is at least
CDR3_MULT
times the number of non-shared differences outside CDR3. The
default value of CDR3_MULT
is 5
. This algorithmic change may be
overridden by using a large value instead, e.g. by CDR3_MULT=100
.
- Change clonotyping algorithm by computing the number
N
in a different and
simpler fashion, as 80^cd
. The old behavior may be obtained by adding the argument
OLD_MULT
.
- Change clonotyping algorithm by preventing merger in cases where light chain constant
regions are different. The old behavior maybe be obtained by adding the argument
OLD_LIGHT
.
- Add lvar
nbc
which is the numerically encoded barcode.
See enclone help lvars
.
11/9/21:
- Add option
NOSPACES
to not show spaces between features specified by the
AMINO
option. See
enclone help amino
.
- Add option
COLOR=codon-diffs
, that causes certain "unchanged" amino acids to
be grayed out. This can make it much easer to see changes. See
enclone help color
.
10/26/21:
- Add
NSEG
and NSEGN
, to allow exclusion of clonotypes having
particular VDJC genes.
- Add
MIN_ORIGINS
.
- Add option
MIN_DONORS
. For example MIN_DONORS=2
only shows
clonotypes containing cells from at least two donors. If you use
MIN_DONORS=2
(or more), MIX_DONORS
will be automatically turned on,
to allow generation of clonotypes having cells from multiple donors.
For all of the above,
please see enclone help filter
.
10/18/21: Allow coloring of honeycomb plots by dataset. Please see
enclone plots.
10/12/21:
- Remove clonotypes that are not placed in a group. This fixes a bug.
- Add symmetric grouping statistics to the summary.
- Fix a bug that caused feature counts to be incorrectly reported if the value for a particular
cell for a particular feature exceeded
65535
. This only happened if the
NH5
option was used.
10/4/21: Add argument MIN_GROUP_DONORS=...
to set a lower bound on the
number of donors contributing to a group, for it to be printed. Please see
enclone help display
.
9/21/21:
- Simplify the install script and expand the installation debugging page. This may resolve some
problems people have had and also provides help in the event that installation fails.
- Add new lead variable
nchains_present
. Please see
enclone help lvars
.
9/20/21:
Add a new default filter called signature filtering that under certain rare circumstances
will decompose complex clonotypes that are incorrectly glued together. This filter can
dramatically affect certain datasets, but has almost no effect on typical data (less than one per
million clonotypes tested).
Please see enclone default filters.
9/17/21:
- Add
KEEP_CLONO_IF_CELL_MIN
. See
enclone help filter
.
- Tweak handling of
NOPRINT PARSEABLE=stdouth
to make columns line up.
9/15/21: Add control over PNG resolution for cell coloring by variable.
9/14/21: Fix some issues with cell coloring, affecting cell coloring by variable and
SPLIT_PLOT_BY_ORIGIN
.
9/11/21: Add the ability to color cells in a honeycomb plot using the values of a variable.
Please see enclone plots.
8/27/21: Add new argument DVARS=...
that can display dataset-level variables,
for now very limited, as described at
see enclone help display
.
In addition, values for GVARS
now appear inside the summary.
8/24/21:
SPLIT_PLOT_BY_ORIGIN
now allows creation of side-by-side honeycomb
plots, representing e.g. different cell types or preparations. See
enclone plots.
- enclone installation now includes a test for whether the correct enclone executable is
accessible from the command line, and prints debugging information if not.
8/17/21: KEEP_CELL_IF
now allows feature variables to appear in constraints,
see enclone help special
.
7/22/21:
- Add option for xy plots to make them symmetric, which is appropriate e.g. for plotting
data from replicates. See enclone plots.
- Add option
INFO_RESOLVE
that modifies INFO
to handle cases where
identical immune receptor sequences have been provided. See
enclone help input
.
7/14/21: Add new arguments HONEY_OUT
and HONEY_IN
to allow
preservation of cell positions between two honeycomb plots of the same data. Please see
enclone plots.
6/30/21: Add cvar cigar
that is the CIGAR string of the V..J contig sequence
versus the universal reference. See
enclone help cvars
.
6/24/21: Now enclone UPDATE
updates to the latest version of enclone.
6/17/21: Add SIM_MAT_PLOT
, to display the pairwise cosine similarity between
a list of variables, see enclone plots.
6/4/21: Tweak the order of default filters so as to increase the likelihood that clonotypes
that are held together tenuously (or not at all) will be pulled apart. This has a tiny effect
on our datasets (changing about 1
in 10^5
clonotypes), but could affect
some user datasets disproportionally.
6/3/21: Fix bug in the computation of datasets_cell
.
6/2/21:
- Allow
PCHAINS=max
. See
enclone help parseable
.
- Add
MAX_HEAVIES=1
to ignore any cell having more than one IGH or TRB chain.
- Fix bug that caused VDJ gene name and id fields to be displayed in parseable output even
when a chain was absent for a given exact subclonotype.
5/6/21: Clonotype grouping has been completely reworked. Please see
enclone help display
.
The pre-existing options are still present but now undocumented, and their behavior might have
changed slightly. We have not optimized the new options for run time, so let us know if there's
a problem and we'll see what we can do.
5/4/21: Several changes that involve D gene assignment, and which allow for the VDDJ case:
- Add cvars
d1_name
, d2_name
, d1_score
,
d2_score
, d_delta
or equivalently d_Δ
, see
enclone help cvars
and
D genes and junction regions
.
- Add options
ALIGN<n>
and JALIGN<n>
to exhibit visual
alignments of V..J sequences or just the junction regions to the concatenated VDJ reference, see
enclone help display
and
D genes and junction regions
.
There are also ALIGN_2ND<n>
and JALIGN_2ND<n>
to use instead the
second best D gene alignments.
- Add global variables
d_inconsistent_%
and d_inconsistent_n
that
provide statistics on overall consistency of D gene assignment, see
enclone help display
and
D genes and junction regions
.
- Add filters
D_INCONSISTENT
to only show clonotypes having an inconsistent D gene
assignment, D_NONE
to show clonotypes have a null D gene assignment, and
D_SECOND
to show only VDDJ clonotypes.
- Add grouping options
GROUP_VJ_REFNAME_HEAVY
and GROUP_VDJ_REFNAME_HEAVY
, see
enclone help display
.
Additionally, the main page on this site now provides links to previous releases of enclone
that match particular releases of Cell Ranger. And there is a new filter MAX_EXACTS
.
4/8/21:
- Fix bug that caused
CONP
to produce the wrong answer in some cases.
- Fix bug that caused FWR4 values to be wrong in some cases.
4/5/21: Add page
enclone default filters
that describes the order of the filters that enclone uses, and provides technical details
about some of the filters, which was previously on the
heuristics page
.
4/2/21:
- Almost any parseable variable can now be used in a linear condition. Of course it doesn't
makes sense to use such a variable unless its values are numeric.
- A number of other restrictions on variables were removed, including by promotion of parseable
variables to lvars or cvars.
- Clicking on the enclone banner at the top of any page on the site now takes you back to
the help section on the main page.
- There is a new
page
that inventories all the enclone variables.
- We turned on overflow checking in the enclone executables. It is possible that you will
now see error messages (tracebacks) where you did not previously see them. Please report
these events!
3/23/21:
- Add new option top plot two variables, see bottom of
enclone plots.
- Add
SOURCE=filename
to import some arguments from another file.
- Add option
SCAN_EXACT
to scan exact subclonotypes rather than clonotypes.
See enclone help filter
.
3/17/21:
- Gene scanning now has an option
SCAN_EXACT
to scan using exact subclonotypes
rather than clonotypes. See
enclone help filter
.
- Add
SOURCE=filename
to read extra arguments from the named file, see
enclone help command
.
3/16/21:
- enclone can now take values for fields associated to particular immune receptor
sequences via
INFO=path.csv
; see
enclone help input
.
- We now allow
TREE=v1,...vn
where the vi
are parseable variables,
resulting in labeling by these variables. See
here. For backward compatibility, const
is translated to const1
. The new display is slightly different than the old
display, showing e.g. const1=IGHG1
rather than IGHG1
.
- There is now a detailed
developers guide
.
3/4/21:
-
Add a plotting option
QUAD_HIVE
that forces honeycomb plots into the first
quadrant. See honeycomb plots.
-
Tweak honeycomb plotting to cause smaller clonotypes to be generally "farther out" than
smaller clonotypes. See honeycomb plots.
-
Add new options
CONX
and CONP
that add amino acid consensus
rows to clonotype tables. Please see
enclone help display
, which refers to
enclone help cvars
.
- For developers, add an option
PROFILE
.
2/14/21: A VDJ reference file can now be tested for defects using a command of the form
enclone REF=<fasta file name>
.
2/13/21:
-
We redesigned the algorithm that determines the columns in clonotype tables,
see notes on heuristics. This addresses some
very rare cases where chains were incorrectly placed in the same column. This also results in
better disintegration of "merged" clonotypes in some cases. There is an additional
change that came about. In rare cases, a cell will have two contigs with identical CDR3 sequences.
This could be the "other" allele or more likely an artifact. Previously one of these contigs
was suppressed in the clonotype table. Now they both appear.
-
For weak chain filtering, we now allow deletion of chains having up to
20
cells,
rather than 5
. See notes on heuristics.
This fixes some pathological examples involving clonotypes having many chains.
-
Added option
FOLD_HEADERS
to reduce horizontal space usage. See also the discussion
of line wrapping in
frequently asked questions
.
2/6/21: Fix the computations of median of a vector. For a vector x
of length
n
, these were computed as x[n/2]
, which is incorrect in the case where
x
has an even number of elements: it should be the mean of the innermost two
elements. However, in cases where the vector elements are integers, we now round this mean up to
the nearest integer, yielding a "rounded median", as the advantage of presenting the exact
median is outweighed by the loss of readability resulting from adding .5
or
.0
to the display.
2/4/21: Add option SUPPRESS_ISOTYPE_LEGEND
.
2/3/21: Add chain variable cdr3_aa_conx
that is the consensus of the
CDR3 amino acid sequences across the clonotype, showing X
for each variant residue,
and cdr3_aa_conp
, which instead of X
shows an amino acid property
symbol. See enclone help cvars
.
We thank Albert Vilella for suggesting these features.
1/19/21: Add lead variables count_cdr1_<regex>
and similar, see
enclone help lvars
.
1/14/21: Add chain variables corresponding to extended or trimmed versions of CDR
sequences, and North versions. Please see
enclone help cvars
.
1/13/21:
- Move onesie merger to a later stage in the process, after certain "junk" deletion steps,
to increase the likelihood of merges happening. This significantly increases the number of
merges, so that after this change, many more clonotypes contain onesies.
- The
BC
argument now may be either a CSV
or TSV
file.
- Automatically find
multi/vdj_b
and multi/vdj_t
subdirectories of
outs.
- Allow
BCR_GEX=p
as a shorthand for BCR=p
and GEX=p
, which
simplifies syntax when a cellranger
multi run is used as input; ditto for
TCR_GEX
.
1/9/21: Following a suggestion of Ganesh Phad, single-cell clonotypes in honeycomb
plots are now localized by color.
1/7/21:
- Greatly speed up honeycomb plots for large numbers of clonotypes.
- Change the installation command to use
bash
rather than sh
to avoid
failures resulting from sh
being instantiated as a different shell.
1/4/21:
-
Fix the output of the parseable variable
cdr3_start<i>
when there was
an insertion earlier in the transcript.
-
Add an option
PLOT_BY_ISOTYPE_COLOR
to allow color specification for the
PLOT_BY_ISOTYPE
argument.
12/14/20: Add option METAX
that allows meta information to be provided on
the command line, rather than through a separate file.
12/9/20:
- Delete the
_ag
antigen feature label (which was documented at
enclone help lvars
) because this
was in fact never supported by cellranger
.
- Change the algorithm for deciding to use a donor reference allele, so that it checks all
donor reference alleles for all V genes having the same name as the one originally assigned to
a contig. In some cases this changes results. Note that this change comes after Cell Ranger
5.0 and with high probability will be integrated into the next major Cell Ranger release.
- Change the default value of
MAX_DIFFS
from 50
to 55
.
Change MAX_DEGRADATION
from 3
to 2
. Change the default
value for MAX_SCORE
from 1,000,000
to 500,000
. Change
the default value for MAX_CDR3_DIFFS
from 10
to 15
.
Ditto comments about Cell Ranger.
- Allow up to 5 (instead of 4) CDR3 amino acid differences when joining chains.
- Find input data correctly if the
cellranger multi
pipeline is used.
- Add a new filter that removes some doublets, and which can be turned off by supplying the
argument
NDOUBLET
(see
enclone help special
and
notes on heuristics).
12/5/20:
-
The argument
F
has been renamed to
KEEP_CLONO_IF_CELL_MEAN
, although for backward compatibility, F
still works. We have added the similar KEEP_CLONO_IF_CELL_MAX
. See
enclone help filter
for both.
-
Rename
FCELL
to KEEP_CELL_IF
, but retain FCELL
for
backward compatibility.
12/2/20: CDR3 sequences are now recomputed by enclone, rather than taken from the value
in all_contig_annotations.json
. This will result in changed values at a very low
frequency, and only if the CDR3 calculation algorithm was changed between the time of the relevant
cellranger
release and the time of the enclone release.
11/24/20:
-
Allow arbitrarily long CDR3 sequences. This change is not part of Cell Ranger 5.0, but may
be part of a subsequent release. In advance of that, in order to exploit this feature, you
will need to add the option
REPROD
to the enclone command line, to cause productive
pairs to be recomputed. Allowing very long CDR3 sequences likely introduces some artifacts. For
example, in human BCR data, we observe CDR3 sequences longer than 40
amino acids at
a rate of about 1/10,000
cells, and these are typically part of a third chain
for a given cell, suggesting that such chains are likely nonproductive. However it may be that
long CDR3 sequences occur as part of productive chains in other species.
-
Add a chain variable
cdr2_aa_ref
the gives the value of the CDR2 amino acids
for the universal reference sequence, and similarly for other cases, see
enclone help cvars
.
11/20/20:
-
Generalize the
FCELL
argument to allow arbitrary expressions. Please see
enclone help special
.
(This is a breaking change.)
11/19/20:
- Add lead variable
count_
that counts the number of occurrences of a given
pattern in the V..J sequences for all chains.
11/4/20:
- Add
SUBSET_JSON
option, which allows construction of a small json file
associated to specified clonotypes, which can be sent to the enclone developers.
- The
NOPRINT
option no longer applies to parseable output generated using
POUT=stdout
or POUT=stdouth
. This change facilitates piping of parseable
output to other programs.
10/20/20: If a variable is of the form abbr:name
, and POUT
is
set to a file name, then the field label that is shown is now abbr
, rather than
abbr:name
. This is really a bug fix.
10/9/20: Add parseable variables for the start and frame of the D region.
9/17/20: Clarify documentation for the case where GEX=(antibody data)
and fix
bug in handling of n_gex
for that.
9/16/20:
-
Test for defective reference sequences and exit if they're found (allowing for override).
There is also a new argument
BUILT_IN
to force recomputation using the built-in
reference (for human or mouse).
- We turned off part of the graph filtering (which can be turned off completely with the
argument
NGRAPH_FILTER
). We did this because in some cases this code was deleting
significant numbers of real cells.
-
Tweak feature computations. The page
this page has been updated accordingly. The
results for tests of species described on that page did not change, but there were changes to
other species, including a few changes for dog and horse.
9/4/20: Add the capability of seeing which default filters would have been applied, if
the filters are turned off. See the lead variable "filter" at
enclone help lvars
.
9/2/20:
- Add options
DIFF_STYLE=C1
and DIFF_STYLE=C2
that allow alternate
labeling for the diff row in a clonotype table, which by default shows x's and dots.
- Fix bugs in the diff row printing: sometimes it was not shown, and it was not correctly
handled when
COLOR=property
was specified.
9/1/20:
- Add parseable field
vj_seq_nl
, the DNA sequence of V..J, but starting after the
leader.
- Add parseable field
vj_aa_nl
, the amino acid sequence of V..J, but starting after
the leader.
- Add chain variable
aa%
= amino acid percent identity with donor reference,
outside junction region.
- Add chain variable
dna%
= nucleotide percent identity with donor reference,
outside junction region.
- Add summary of barcode fate if SUMMARY option is used.
8/31/20: add FWR4 support
8/28/20: add new filters CONST_IGH
and CONST_IGKL
that allow
filtering of cells by isotype. Please see
enclone help special
.
8/27/20:
-
Fix bugs in reporting of insertions in the notes field.
-
Now CDR1, CDR2, FWR1, FWR2 and FWR3 can be can be computed and displayed. Please see
enclone help amino
and enclone help cvars
for how to specify these, and
this page for how we calculate these features.
8/24/20:
- Add lead variable
dref_aa
, the number of amino acid differences
with the donor reference.
- Add estimated doublet rate to summary stats.
- We are deprecating the lead variables
sec
and mem
that measure
UMIs supporting secreted versus membrane-bound antibody transcripts. Because the exon boundaries
that determine this are far from the 5' end, there is rarely enough signal to be informative.
We removed the documentation.
8/20/20:
- Allow "Levenshtein distance patterns" for CDR3 filter specification. For more information,
type or click here:
enclone help filter
.
- Change what the weak onesies filter does: unless
NWEAK_ONESIES
is used, now,
rather than delete certain dubious onesie clonotypes, such clonotypes are disintegrated into
single cell clonotypes.
- Change what the improper filter does: unless
NIMPROPER
is used, now,
clonotypes having more than one chain but all of the same type are deleted.
- Add a new filter that prevents merges of onesie clonotypes into other clonotypes; this
filter may be turned off with a new argument
NMERGE_ONESIES
. This behavior is
mostly (but not completely) a splitting out of previous functionality so as to simplify and
clarify.
Importantly, the last three changes have the effect of increasing the number of cells in
clonotypes; the extra cells are mostly in onesie clonotypes.
Precise definitions may be found by typing (or clicking here):
enclone help special
.
8/17/20: deprecate KEEP_IMPROPER
; the new name is
NIMPROPER
.
8/10/20: tweak the definition of the weak onesies filter so that it does not
delete single-cell clonotypes. Superceded by subsequent change on 8/18/20.
8/7/20: add the ability to analyze alternate splicing using GEX data to characterize
UMIs as secreted or membrane, and display this information using lvars "sec" and "mem". See
enclone help lvars
for limitations. This is highly experimental.
8/5/20:
- A reference file is now required as part of the Cell Ranger outs directory,
if Cell Ranger version 4.0 or greater was used.
- Deprecate
MAX_SCORE
and replace by MAX_LOG_SCORE
, the
base 10 logarithm of it.
- Add cvar
cdr3_len
- Add and document knobs that allow nearly all clonotype join filtering to be turned off. Please
see "enclone help how" and the end of "enclone help faq".
6/24/20:
- Add support for iNKT and MAIT cells.
- Make enclone faster. This is most noticeable in cases where many GEX datasets are
provided as input.
6/19/20:
- We now use a data hierarchy of donor (top), origin, dataset (bottom), where an
origin is a set of 1 or more datasets from the same source (tube of cells, tissue, timepoint, etc.).
(This breaks previous invocations of
META
.)
- Improve the alternate (faster) internal storage structure for the GEX matrix
created using the option
NH5
as described using the command
enclone help input
.
This will speed things up, particularly for the case where several datasets are combined. If
you have already used the NH5
option for a given dataset, then the next time you
run enclone on it, the file will be automatically rewritten. This would also apply to some
datasets obtained as part of the large
download.
6/17/20:
- Now
TREE=const
can be used to show a tree with heavy chain constant region
names attached to the leaves.
SEG
and SEGN
are now cumulative, so that multiple instances may
be used to progressively filter.
- The clonotype joining heuristic parameters
MAX_SCORE
and
MAX_CDR3_DIFFS
are now accessible.
6/10/20:
- Add a complex of features for generating phylogenetic trees from clonotypes, see
here.
- New "single button" installation procedure.
- Change the default value for
PRE
to ~/enclone/datasets,~/enclone/datasets2
.
- Add argument
NALL
to turn off all filters.
- Add new lead variables
nd<k>
that display the number of cells in the
top datasets for a given clonotype.
- Add new lead variable
dref
that shows the distance of V..J from the reference
outside the region of recombination.
- Add argument
COMPLETE
to remove exact subclonotypes that do not have all
chains.
- Test for consistency between VDJ and GEX barcodes, and exit if this is not the case.
- Add option
COLOR=property
to color amino acids by their properties.
- Add option
FCELL
to allow filtering by cells.
5/29/20:
Add new "UMI ratio" filter that further reduces noise in certain cases. This can be turned
off using the argument NUMI_RATIO
.
5/22/20:
Add major new "UMI" filter that greatly reduces noise in certain cases. This can be turned
off using the argument NUMI
.
5/12/20:
Add PLOT_BY_ISOTYPE
to generate honeycomb plots colored by isotype.
5/1/20:
Change the definition of the fields "edit" and "comp" to be based on
alignment from the beginning of the CDR3 up to the end of the J, rather than stopping at
the end of the CDR3. The intention is to capture the full region of recombination, which
may not have been done before.
4/30/20:
First release.